User contributions
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- 10:40, 27 July 2016 (diff | hist) . . (+129) . . BUSCO
- 10:31, 27 July 2016 (diff | hist) . . (+196) . . BUSCO
- 10:02, 27 July 2016 (diff | hist) . . (+22) . . BUSCO
- 10:00, 27 July 2016 (diff | hist) . . (+58) . . BUSCO
- 18:31, 26 July 2016 (diff | hist) . . (+238) . . BUSCO
- 18:30, 26 July 2016 (diff | hist) . . (+1) . . Augustus
- 18:29, 26 July 2016 (diff | hist) . . (+245) . . Augustus
- 17:25, 26 July 2016 (diff | hist) . . (+18) . . Augustus
- 15:39, 26 July 2016 (diff | hist) . . (+222) . . N Augustus (Created page with "= Introduction = Worthy gene prediction program from Mario Stanke at Greifenswald. = Admin notes only= == Compilation == Is a simple "make" but the Makefiles (especially t...")
- 15:37, 26 July 2016 (diff | hist) . . (+15) . . Main Page
- 13:05, 26 July 2016 (diff | hist) . . (+10) . . BUSCO
- 11:09, 22 July 2016 (diff | hist) . . (+302) . . BUSCO
- 11:04, 22 July 2016 (diff | hist) . . (+340) . . N BUSCO (Created page with "= Introduction = BUSCO, like Cegma, is a special tool for the field of "completeness assessment". This concerns genome assemblies, particularly ones generated de-novo, when b...")
- 10:57, 22 July 2016 (diff | hist) . . (+12) . . Main Page
- 17:13, 21 July 2016 (diff | hist) . . (-2) . . Cegma (current)
- 17:11, 21 July 2016 (diff | hist) . . (+5,160) . . N Cegma (Created page with " = How to use Cegma= By default, Cegma expects that you will only analyse one fasta sequence each time. So it has certain standard names for its output files which '''do not...")
- 17:09, 21 July 2016 (diff | hist) . . (+12) . . Main Page
- 08:18, 20 July 2016 (diff | hist) . . (+103) . . Srst2
- 17:13, 19 July 2016 (diff | hist) . . (+10) . . Srst2
- 17:12, 19 July 2016 (diff | hist) . . (+825) . . Srst2
- 16:55, 19 July 2016 (diff | hist) . . (+95) . . Srst2
- 15:59, 19 July 2016 (diff | hist) . . (+18) . . Srst2
- 15:58, 19 July 2016 (diff | hist) . . (-35) . . Srst2
- 15:50, 19 July 2016 (diff | hist) . . (+182) . . Srst2
- 15:15, 19 July 2016 (diff | hist) . . (+42) . . Patric (→Introduction) (current)
- 15:15, 19 July 2016 (diff | hist) . . (+754) . . N Patric (Created page with "= Introduction = = Guide = * Registering for Patric is a good idea. * When browsing you have an implicit workspace. You add items to it if you are interested in them. * The...")
- 15:07, 19 July 2016 (diff | hist) . . (+1) . . Main Page
- 15:07, 19 July 2016 (diff | hist) . . (+50) . . Main Page
- 18:01, 18 July 2016 (diff | hist) . . (+92) . . Miseq Prokaryote FASTQ analysis (current)
- 17:47, 18 July 2016 (diff | hist) . . (+22) . . Miseq Prokaryote FASTQ analysis
- 17:46, 18 July 2016 (diff | hist) . . (+262) . . Miseq Prokaryote FASTQ analysis
- 17:43, 18 July 2016 (diff | hist) . . (+9) . . Miseq Prokaryote FASTQ analysis
- 17:40, 18 July 2016 (diff | hist) . . (+20) . . Miseq Prokaryote FASTQ analysis
- 17:29, 18 July 2016 (diff | hist) . . (+2) . . Miseq Prokaryote FASTQ analysis
- 17:27, 18 July 2016 (diff | hist) . . (+11) . . Miseq Prokaryote FASTQ analysis
- 17:26, 18 July 2016 (diff | hist) . . (+2) . . Miseq Prokaryote FASTQ analysis
- 17:24, 18 July 2016 (diff | hist) . . (+571) . . Miseq Prokaryote FASTQ analysis
- 17:16, 18 July 2016 (diff | hist) . . (0) . . Miseq Prokaryote FASTQ analysis
- 17:15, 18 July 2016 (diff | hist) . . (+581) . . N Miseq Prokaryote FASTQ analysis (Created page with "=Introduction= We have our own Miseq machine and each week a run is carried out (each run costs about £1000 in consumibles) from various samples. They are unloaded onto HDR...")
- 17:09, 18 July 2016 (diff | hist) . . (+38) . . Main Page
- 17:55, 13 July 2016 (diff | hist) . . (+3) . . Srst2
- 18:39, 7 July 2016 (diff | hist) . . (+169) . . SPAdes
- 16:43, 6 July 2016 (diff | hist) . . (+2,538) . . FASTQC and MultiQC
- 16:43, 6 July 2016 (diff | hist) . . (+183) . . FASTQC and MultiQC
- 16:32, 6 July 2016 (diff | hist) . . (+5,010) . . N FASTQC and MultiQC (Created page with "=Introduction= Quality visualization = Help file = SYNOPSIS fastqc seqfile1 seqfile2 .. seqfileN fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam] [-c...")
- 16:32, 6 July 2016 (diff | hist) . . (+12) . . Main Page
- 15:44, 6 July 2016 (diff | hist) . . (+1) . . FASTQC (current)
- 15:44, 6 July 2016 (diff | hist) . . (+1) . . FASTQC
- 15:43, 6 July 2016 (diff | hist) . . (-7) . . FASTQC
- 15:43, 6 July 2016 (diff | hist) . . (+5,015) . . N FASTQC (Created page with "=Introduction= Quality visualization = Help file = SYNOPSIS fastqc seqfile1 seqfile2 .. seqfileN fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam]...")
- 15:42, 6 July 2016 (diff | hist) . . (+13) . . Main Page
- 18:17, 5 July 2016 (diff | hist) . . (+317) . . Trimmomatic (current)
- 18:06, 5 July 2016 (diff | hist) . . (+53) . . Trimmomatic
- 18:05, 5 July 2016 (diff | hist) . . (+171) . . Trimmomatic
- 15:54, 5 July 2016 (diff | hist) . . (+550) . . Trimmomatic
- 18:01, 2 July 2016 (diff | hist) . . (-3) . . SPAdes
- 18:01, 2 July 2016 (diff | hist) . . (+126) . . SPAdes
- 16:36, 2 July 2016 (diff | hist) . . (+149) . . SPAdes
- 17:47, 1 July 2016 (diff | hist) . . (+735) . . SPAdes
- 17:16, 1 July 2016 (diff | hist) . . (+613) . . SPAdes
- 14:57, 30 June 2016 (diff | hist) . . (-2) . . Calculating coverage
- 14:53, 30 June 2016 (diff | hist) . . (+40) . . Calculating coverage
- 14:03, 30 June 2016 (diff | hist) . . (+663) . . Calculating coverage
- 17:12, 29 June 2016 (diff | hist) . . (+324) . . N Trimmomatic (Created page with "=Introduction= = Example use-cases= java -jar $PATHTRIMMOJAR/trimmomatic-0.32.jar PE -threads 6 -phred33 $DATASETPATH/Pair1.fastq.gz $DATASETPATH/Pair1.fastq.gz forward_pai...")
- 17:03, 29 June 2016 (diff | hist) . . (+18) . . Main Page
- 16:19, 29 June 2016 (diff | hist) . . (+164) . . 6TB storage expansion
- 16:05, 29 June 2016 (diff | hist) . . (+1,183) . . 6TB storage expansion
- 15:37, 29 June 2016 (diff | hist) . . (+754) . . 6TB storage expansion
- 15:28, 29 June 2016 (diff | hist) . . (+571) . . 6TB storage expansion
- 14:54, 29 June 2016 (diff | hist) . . (+90) . . 6TB storage expansion
- 14:50, 29 June 2016 (diff | hist) . . (+2) . . 6TB storage expansion
- 14:48, 29 June 2016 (diff | hist) . . (+3,259) . . 6TB storage expansion
- 14:42, 29 June 2016 (diff | hist) . . (+87) . . 6TB storage expansion
- 14:38, 29 June 2016 (diff | hist) . . (+7) . . 6TB storage expansion
- 14:38, 29 June 2016 (diff | hist) . . (+1,892) . . 6TB storage expansion
- 12:24, 29 June 2016 (diff | hist) . . (-1) . . 6TB storage expansion
- 12:13, 29 June 2016 (diff | hist) . . (+21) . . Samtools
- 12:06, 29 June 2016 (diff | hist) . . (+84) . . Samtools
- 10:57, 29 June 2016 (diff | hist) . . (+124) . . Samtools
- 10:32, 29 June 2016 (diff | hist) . . (+310) . . Samtools
- 18:31, 28 June 2016 (diff | hist) . . (-4) . . Main Page
- 18:23, 28 June 2016 (diff | hist) . . (-130) . . 6TB storage expansion
- 18:23, 28 June 2016 (diff | hist) . . (+226) . . 6TB storage expansion
- 17:53, 28 June 2016 (diff | hist) . . (+48) . . Calculating coverage
- 17:48, 28 June 2016 (diff | hist) . . (+300) . . N Calculating coverage (Created page with "= Introduction = Coverage can be calculated in several different ways and this pages aims to describe a few of them = Bedtools genomecov = This is one of the most commonly...")
- 17:16, 28 June 2016 (diff | hist) . . (+216) . . Main Page
- 13:42, 28 June 2016 (diff | hist) . . (+18) . . CallSNPs.py
- 14:35, 27 June 2016 (diff | hist) . . (+26) . . Samtools
- 14:18, 27 June 2016 (diff | hist) . . (-359) . . Main Page
- 14:17, 27 June 2016 (diff | hist) . . (+346) . . Main Page
- 16:21, 23 June 2016 (diff | hist) . . (+85) . . 6TB storage expansion
- 16:19, 23 June 2016 (diff | hist) . . (+111) . . 6TB storage expansion
- 16:14, 23 June 2016 (diff | hist) . . (+241) . . 6TB storage expansion
- 16:12, 23 June 2016 (diff | hist) . . (+58) . . 6TB storage expansion
- 16:04, 23 June 2016 (diff | hist) . . (+309) . . 6TB storage expansion (→= interpreter)
- 15:55, 23 June 2016 (diff | hist) . . (+161) . . 6TB storage expansion
- 15:45, 23 June 2016 (diff | hist) . . (+5,102) . . N BamQC (Created page with "= Introduction = From S. Andrews' lab, who also produce FastQC = Helpfile output = BamQC - A high throughput mapped sequence QC analysis tool SYNOPSIS ba...") (current)
- 15:44, 23 June 2016 (diff | hist) . . (+12) . . Main Page
- 15:32, 23 June 2016 (diff | hist) . . (+14) . . Main Page
- 14:48, 23 June 2016 (diff | hist) . . (+45) . . 6TB storage expansion
- 14:00, 23 June 2016 (diff | hist) . . (+24) . . 6TB storage expansion
- 13:58, 23 June 2016 (diff | hist) . . (+285) . . 6TB storage expansion
- 13:44, 23 June 2016 (diff | hist) . . (+99) . . SPAdes
- 13:37, 23 June 2016 (diff | hist) . . (+218) . . 6TB storage expansion (→Tools)
- 13:25, 23 June 2016 (diff | hist) . . (+2) . . 6TB storage expansion
- 13:24, 23 June 2016 (diff | hist) . . (+365) . . 6TB storage expansion
- 13:16, 23 June 2016 (diff | hist) . . (+130) . . 6TB storage expansion (→Links)
- 13:15, 23 June 2016 (diff | hist) . . (+280) . . 6TB storage expansion
- 13:11, 23 June 2016 (diff | hist) . . (+235) . . N Frontend Restart (Created page with "= Introduction = Contains notes on how to restart marvin. = Provisos = Restarting marvin is a major operation, as all running jobs are lost. It is therefore necessary to a...")
- 13:06, 23 June 2016 (diff | hist) . . (+23) . . Main Page
- 12:28, 23 June 2016 (diff | hist) . . (+262) . . N CAFE (Created page with "= Introduction = Matthew Hahn's software for detecting evolution (rise/demise) of gene families. Operationally, it seems somewhat unusual, as it has an interpreter. There a...") (current)
- 12:26, 23 June 2016 (diff | hist) . . (+13) . . Main Page
- 15:01, 22 June 2016 (diff | hist) . . (+19) . . Main Page
- 23:40, 21 June 2016 (diff | hist) . . (+156) . . OrthoFinder (current)
- 23:38, 21 June 2016 (diff | hist) . . (+3,556) . . OrthoFinder
- 22:46, 21 June 2016 (diff | hist) . . (+110) . . OrthoFinder
- 22:06, 21 June 2016 (diff | hist) . . (+19,663) . . OrthoFinder
- 21:41, 21 June 2016 (diff | hist) . . (+99) . . N OrthoFinder (Created page with "= Introduction = An orthology finder seen in some circles as better than the widely used OrthoMCL.")
- 21:39, 21 June 2016 (diff | hist) . . (+1) . . Main Page
- 21:34, 21 June 2016 (diff | hist) . . (+17) . . Main Page
- 13:09, 21 June 2016 (diff | hist) . . (+229) . . N 6TB storage expansion (Created page with "= Introduction = 56 instead of 50TB are now available for the bioinformatics cluster. The tasks required to realize this extra space are: * rescan multipath, details: multipa...")
- 12:26, 21 June 2016 (diff | hist) . . (+28) . . Main Page
- 17:34, 14 June 2016 (diff | hist) . . (+291) . . Node1 issues
- 16:18, 14 June 2016 (diff | hist) . . (+463) . . Node1 issues
- 16:06, 14 June 2016 (diff | hist) . . (+142) . . Node1 issues
- 16:01, 14 June 2016 (diff | hist) . . (+1,445) . . Node1 issues
- 15:58, 14 June 2016 (diff | hist) . . (+84) . . Node1 issues
- 15:50, 14 June 2016 (diff | hist) . . (+51) . . Node1 issues
- 15:45, 14 June 2016 (diff | hist) . . (+2,525) . . Node1 issues
- 15:34, 14 June 2016 (diff | hist) . . (+446) . . Node1 issues
- 15:28, 14 June 2016 (diff | hist) . . (+391) . . N Node1 issues (Created page with "=Red Hat Subscription issues= At some point in March 2016, node1 was not conencting to the repositories properly. the command subscription-manager identity After this, I go...")
- 15:23, 14 June 2016 (diff | hist) . . (+19) . . Main Page
- 16:23, 10 June 2016 (diff | hist) . . (+304) . . N Users and Groups (Created page with "= Introduction= Some, not all, of the tips for setting up users and groups. = * Groups often need to be set up in smbldap, but not always. It's desired because it means al...")
- 16:16, 10 June 2016 (diff | hist) . . (+23) . . Main Page
- 22:08, 9 June 2016 (diff | hist) . . (+307) . . Sra-tools
- 12:55, 9 June 2016 (diff | hist) . . (+64) . . Kallisto (current)
- 12:35, 9 June 2016 (diff | hist) . . (+1) . . CMake (current)
- 12:16, 9 June 2016 (diff | hist) . . (+45) . . CMake
- 12:14, 9 June 2016 (diff | hist) . . (+130) . . CMake
- 12:00, 9 June 2016 (diff | hist) . . (0) . . CMake
- 11:59, 9 June 2016 (diff | hist) . . (+382) . . CMake
- 10:30, 9 June 2016 (diff | hist) . . (+327) . . CMake
- 10:03, 9 June 2016 (diff | hist) . . (+429) . . N CMake (Created page with "= Introduction = Cmake is a compilation configuration platform which promises cross platform portability. I.e. it is apparently able to compile for Linux, MacOSX and Windows....")
- 09:39, 9 June 2016 (diff | hist) . . (+12) . . Main Page
- 22:41, 8 June 2016 (diff | hist) . . (+8) . . Samtools
- 22:13, 8 June 2016 (diff | hist) . . (+178) . . Samtools
- 14:36, 8 June 2016 (diff | hist) . . (-2) . . Samtools
- 13:47, 8 June 2016 (diff | hist) . . (+87) . . Samtools
- 13:28, 8 June 2016 (diff | hist) . . (+187) . . Samtools
- 13:26, 8 June 2016 (diff | hist) . . (+622) . . Samtools
- 13:18, 8 June 2016 (diff | hist) . . (+322) . . N Samtools (Created page with "=Introduction= Samtools hardly needs an introduction, it is one of the cornerstones of bioinformatics processing. Primarily this is due to its providing various tools (avail...")
- 13:09, 8 June 2016 (diff | hist) . . (+15) . . Main Page
- 16:58, 7 June 2016 (diff | hist) . . (+90) . . Prokka
- 16:57, 7 June 2016 (diff | hist) . . (+4,898) . . Prokka
- 16:33, 7 June 2016 (diff | hist) . . (+66) . . N Prokka (Created page with "= Introduction = genome annotator for bacterial circular genomes.")
- 16:32, 7 June 2016 (diff | hist) . . (+13) . . Main Page
- 15:52, 7 June 2016 (diff | hist) . . (+103) . . Abacas (current)
- 14:36, 7 June 2016 (diff | hist) . . (+97) . . MUMmer (current)
- 14:32, 7 June 2016 (diff | hist) . . (+45) . . N MUMmer (Created page with "=Introduction= maximal matching =Use-cases=")
- 14:32, 7 June 2016 (diff | hist) . . (+13) . . Main Page
- 13:30, 7 June 2016 (diff | hist) . . (+1) . . Abacas
- 13:29, 7 June 2016 (diff | hist) . . (+2,559) . . Abacas
- 12:16, 7 June 2016 (diff | hist) . . (0) . . Abacas
- 12:15, 7 June 2016 (diff | hist) . . (+674) . . N Abacas (Created page with "=Introduction= algorithm-based automatic contiguation of assembled sequences = Basic usage = First, load the software module load abacas Then, make a folder with the refe...")
- 12:10, 7 June 2016 (diff | hist) . . (+13) . . Main Page
- 23:24, 26 May 2016 (diff | hist) . . (+111) . . Kallisto
- 23:23, 26 May 2016 (diff | hist) . . (+426) . . Kallisto
- 22:29, 26 May 2016 (diff | hist) . . (+457) . . Kallisto
- 22:25, 26 May 2016 (diff | hist) . . (+383) . . Kallisto
- 17:47, 26 May 2016 (diff | hist) . . (+262) . . Kallisto
- 17:38, 26 May 2016 (diff | hist) . . (+310) . . Kallisto
- 17:25, 26 May 2016 (diff | hist) . . (-124) . . Kallisto
- 17:11, 26 May 2016 (diff | hist) . . (+341) . . Kallisto
- 14:31, 26 May 2016 (diff | hist) . . (+1) . . Kallisto
- 23:45, 25 May 2016 (diff | hist) . . (0) . . Kallisto
- 23:45, 25 May 2016 (diff | hist) . . (+215) . . Kallisto
- 23:43, 25 May 2016 (diff | hist) . . (+322) . . Kallisto
- 22:58, 25 May 2016 (diff | hist) . . (+387) . . Sra-tools
- 22:47, 25 May 2016 (diff | hist) . . (+321) . . Edgen RNAseq (current)
- 22:21, 25 May 2016 (diff | hist) . . (+804) . . Edgen RNAseq
- 22:08, 25 May 2016 (diff | hist) . . (+648) . . Edgen RNAseq
- 21:57, 25 May 2016 (diff | hist) . . (+26) . . Kallisto
- 21:53, 25 May 2016 (diff | hist) . . (+96) . . Kallisto
- 21:51, 25 May 2016 (diff | hist) . . (+60) . . Kallisto
- 21:37, 25 May 2016 (diff | hist) . . (+282) . . Kallisto
- 17:05, 25 May 2016 (diff | hist) . . (+161) . . Kallisto
- 16:54, 25 May 2016 (diff | hist) . . (+117) . . Kallisto
- 15:30, 24 May 2016 (diff | hist) . . (+284) . . BLAST
- 15:26, 24 May 2016 (diff | hist) . . (+602) . . BLAST
- 15:21, 24 May 2016 (diff | hist) . . (+18) . . Two Eel Scaffolds (current)
- 14:19, 24 May 2016 (diff | hist) . . (-148) . . Two Eel Scaffolds
- 23:31, 23 May 2016 (diff | hist) . . (+180) . . Kallisto
- 00:09, 23 May 2016 (diff | hist) . . (+305) . . Kallisto
- 00:00, 23 May 2016 (diff | hist) . . (-155) . . Two Eel Scaffolds
- 23:17, 22 May 2016 (diff | hist) . . (+97) . . N Edgen RNAseq (Created page with "= Introduction = This is based on Edinburgh Genomics' two day RNAseq course. = Steps in Brief =")
- 23:09, 22 May 2016 (diff | hist) . . (+19) . . Main Page
- 23:09, 22 May 2016 (diff | hist) . . (+283) . . Kallisto
- 16:47, 22 May 2016 (diff | hist) . . (-147) . . Trinity Protocol
- 15:24, 22 May 2016 (diff | hist) . . (-318) . . Trinity Protocol
- 16:46, 18 May 2016 (diff | hist) . . (+7) . . Srst2
- 23:34, 17 May 2016 (diff | hist) . . (+179) . . SPAdes
- 23:07, 17 May 2016 (diff | hist) . . (0) . . SPAdes
- 15:53, 17 May 2016 (diff | hist) . . (+366) . . Stacks (→Example command-lines)
- 15:47, 17 May 2016 (diff | hist) . . (+155) . . Stacks
- 15:37, 17 May 2016 (diff | hist) . . (+69) . . Stacks
- 15:35, 17 May 2016 (diff | hist) . . (+252) . . Stacks
- 15:30, 17 May 2016 (diff | hist) . . (0) . . Stacks
- 15:29, 17 May 2016 (diff | hist) . . (+1) . . Stacks
- 15:13, 17 May 2016 (diff | hist) . . (+400) . . Stacks
- 12:55, 17 May 2016 (diff | hist) . . (-18) . . Srst2
- 12:54, 17 May 2016 (diff | hist) . . (+576) . . Srst2
- 00:11, 17 May 2016 (diff | hist) . . (+255) . . Srst2
- 00:08, 17 May 2016 (diff | hist) . . (+1) . . Srst2
- 00:07, 17 May 2016 (diff | hist) . . (+485) . . Srst2
- 22:28, 15 May 2016 (diff | hist) . . (+182) . . Two Eel Scaffolds
- 22:11, 15 May 2016 (diff | hist) . . (-2) . . Two Eel Scaffolds
- 22:10, 15 May 2016 (diff | hist) . . (+1) . . Two Eel Scaffolds
- 22:09, 15 May 2016 (diff | hist) . . (+260) . . Two Eel Scaffolds
- 22:07, 15 May 2016 (diff | hist) . . (+199) . . Two Eel Scaffolds
- 22:05, 15 May 2016 (diff | hist) . . (+35) . . BLAST
- 22:04, 15 May 2016 (diff | hist) . . (+523) . . BLAST
- 21:50, 15 May 2016 (diff | hist) . . (+683) . . Two Eel Scaffolds
- 21:39, 15 May 2016 (diff | hist) . . (+1,551) . . BLAST
- 21:34, 15 May 2016 (diff | hist) . . (+484) . . BLAST
- 21:16, 15 May 2016 (diff | hist) . . (-17) . . BLAST
- 21:15, 15 May 2016 (diff | hist) . . (+442) . . BLAST
- 21:10, 15 May 2016 (diff | hist) . . (+5) . . BLAST
- 17:18, 15 May 2016 (diff | hist) . . (+60) . . Two Eel Scaffolds (→pdcd10b's 7 exons against eelScaffold32)
- 17:13, 15 May 2016 (diff | hist) . . (+209) . . Two Eel Scaffolds (→pdcd10b's 7 exons against eelScaffold32)
- 01:28, 15 May 2016 (diff | hist) . . (+76) . . Two Eel Scaffolds
- 01:27, 15 May 2016 (diff | hist) . . (+22) . . Two Eel Scaffolds
- 01:26, 15 May 2016 (diff | hist) . . (+53) . . Two Eel Scaffolds
- 01:20, 15 May 2016 (diff | hist) . . (+533) . . Two Eel Scaffolds
- 16:41, 13 May 2016 (diff | hist) . . (-157) . . Two Eel Scaffolds
- 16:38, 13 May 2016 (diff | hist) . . (+153) . . Two Eel Scaffolds
- 16:09, 13 May 2016 (diff | hist) . . (+2) . . Two Eel Scaffolds
- 16:08, 13 May 2016 (diff | hist) . . (+40) . . Two Eel Scaffolds (→pdcd10b's 7 exons against eelScaffold32)
- 16:04, 13 May 2016 (diff | hist) . . (+39) . . Two Eel Scaffolds (→pdcd10b's 7 exons against eelScaffold320)
- 16:02, 13 May 2016 (diff | hist) . . (+4,814) . . Two Eel Scaffolds
- 15:38, 13 May 2016 (diff | hist) . . (+40) . . Two Eel Scaffolds (→pdcd10b's 7 exons against eelScaffold320)
- 15:37, 13 May 2016 (diff | hist) . . (+89) . . Two Eel Scaffolds (→nrd1a's 37 exons against eelScaffold32)
- 15:36, 13 May 2016 (diff | hist) . . (+47) . . Two Eel Scaffolds
- 15:34, 13 May 2016 (diff | hist) . . (+6,733) . . Two Eel Scaffolds
- 15:22, 13 May 2016 (diff | hist) . . (+170) . . Two Eel Scaffolds
- 13:31, 13 May 2016 (diff | hist) . . (+217) . . Two Eel Scaffolds
- 12:56, 13 May 2016 (diff | hist) . . (+115) . . Two Eel Scaffolds
- 12:52, 13 May 2016 (diff | hist) . . (+150) . . Two Eel Scaffolds
- 17:03, 12 May 2016 (diff | hist) . . (-26) . . Two Eel Scaffolds
- 16:50, 12 May 2016 (diff | hist) . . (+45) . . Cluster Manual
- 16:41, 12 May 2016 (diff | hist) . . (+333) . . Cluster Manual
- 16:31, 12 May 2016 (diff | hist) . . (+18) . . CallSNPs.py
- 16:30, 12 May 2016 (diff | hist) . . (+91) . . CallSNPs.py
- 16:11, 12 May 2016 (diff | hist) . . (+38) . . Two Eel Scaffolds
- 16:10, 12 May 2016 (diff | hist) . . (+61) . . Two Eel Scaffolds
- 16:09, 12 May 2016 (diff | hist) . . (+132) . . Two Eel Scaffolds
- 15:21, 12 May 2016 (diff | hist) . . (+346) . . Two Eel Scaffolds
- 15:15, 12 May 2016 (diff | hist) . . (+682) . . N Two Eel Scaffolds (Created page with "= Introduction = Two DNA scaffolds are presented: # '''eelScaffold32'''. 679 422 bp and 42.25% GC. # '''eelScaffold320'''. 246 433 bp and 43.47% GC. In terms special geens o...")
- 14:31, 12 May 2016 (diff | hist) . . (+44) . . Main Page
- 13:54, 12 May 2016 (diff | hist) . . (+1) . . Ensembl (current)
- 13:51, 12 May 2016 (diff | hist) . . (+157) . . Ensembl
- 13:47, 12 May 2016 (diff | hist) . . (+178) . . Ensembl (→Variant Effect Predictor)
- 13:33, 12 May 2016 (diff | hist) . . (+4,033) . . Ensembl (→Variant Effect Predictor)
- 12:28, 12 May 2016 (diff | hist) . . (+1) . . Admin Tips (→Simple commands on all nodes, giving node name)
- 12:28, 12 May 2016 (diff | hist) . . (+52) . . Admin Tips
- 12:27, 12 May 2016 (diff | hist) . . (+125) . . N Admin Tips (Created page with " ==Simple commands on all nodes, giving node name == for i in node{1..10}; do ssh $i 'echo -n "$HOSTNAME: "; uname -a';done")
- 12:26, 12 May 2016 (diff | hist) . . (+17) . . Main Page
- 17:07, 11 May 2016 (diff | hist) . . (+224) . . Ensembl
- 15:23, 11 May 2016 (diff | hist) . . (+222) . . Ensembl
- 15:00, 11 May 2016 (diff | hist) . . (+72) . . Ensembl
- 14:42, 11 May 2016 (diff | hist) . . (+75) . . Ensembl
- 14:39, 11 May 2016 (diff | hist) . . (-7) . . Ensembl
- 14:39, 11 May 2016 (diff | hist) . . (+258) . . Ensembl
- 14:36, 11 May 2016 (diff | hist) . . (+585) . . N Ensembl (Created page with "= Introduction = Ensembl produces a range of utilities and tools, most especially, an API. It is mostly a perl endeavour, though a RESTful API is alsof available, although t...")
- 14:30, 11 May 2016 (diff | hist) . . (+15) . . Main Page
- 16:07, 10 May 2016 (diff | hist) . . (+492) . . Stacks
- 16:07, 10 May 2016 (diff | hist) . . (-493) . . SPAdes
- 16:07, 10 May 2016 (diff | hist) . . (+93) . . SPAdes
- 16:06, 10 May 2016 (diff | hist) . . (+400) . . SPAdes
- 15:19, 10 May 2016 (diff | hist) . . (+89) . . SPAdes
- 15:17, 10 May 2016 (diff | hist) . . (+557) . . SPAdes
- 14:20, 10 May 2016 (diff | hist) . . (+389) . . SPAdes
- 18:19, 9 May 2016 (diff | hist) . . (+110) . . RedHat (→Installation of devtoolset-2)
- 17:59, 9 May 2016 (diff | hist) . . (+47) . . RedHat
- 17:57, 9 May 2016 (diff | hist) . . (+506) . . RedHat (→Installation of devtoolset-2)
- 17:42, 9 May 2016 (diff | hist) . . (+308) . . RedHat
- 17:39, 9 May 2016 (diff | hist) . . (0) . . RedHat
- 17:39, 9 May 2016 (diff | hist) . . (+54) . . RedHat
- 17:38, 9 May 2016 (diff | hist) . . (0) . . RedHat
- 17:09, 9 May 2016 (diff | hist) . . (+148) . . N RedHat (Created page with "StAB subscribes to Red Hat = outdated repomd.xml warnings= You can get rid of them (i.e. updaet the repond.xml) by: yum clean all yum update yum*")
- 17:00, 9 May 2016 (diff | hist) . . (+13) . . Main Page
- 16:09, 9 May 2016 (diff | hist) . . (+8) . . Stacks
- 15:59, 9 May 2016 (diff | hist) . . (+136) . . Stacks
- 15:57, 9 May 2016 (diff | hist) . . (+187) . . Stacks
- 15:51, 9 May 2016 (diff | hist) . . (+154) . . Stacks
- 17:52, 6 May 2016 (diff | hist) . . (+89) . . PGAP (current)
- 17:48, 6 May 2016 (diff | hist) . . (+345) . . PGAP
- 17:00, 6 May 2016 (diff | hist) . . (+236) . . PGAP
- 16:46, 6 May 2016 (diff | hist) . . (+150) . . PGAP (→Step 3 Running PGAP)
- 16:40, 6 May 2016 (diff | hist) . . (+390) . . N PGAP (Created page with "= Introduction = = Usage = == Step 3 Running PGAP == For PAGP, there are five functional modules: * cluster analysis of functional genes * pan-genome profile analysis * ge...")
- 16:39, 6 May 2016 (diff | hist) . . (+11) . . Main Page
- 15:03, 5 May 2016 (diff | hist) . . (-12) . . Main Page
- 15:03, 5 May 2016 (diff | hist) . . (+12) . . Main Page
- 23:54, 4 May 2016 (diff | hist) . . (+209) . . JBrowse
- 23:52, 4 May 2016 (diff | hist) . . (+613) . . N JBrowse (Created page with "=Introduction= Quick Javascript based Genome Viewer = Using = Like other browsers, JBrowse simply gives a visual way of navigating a set of sequences. * Beside the magnify...")
- 23:45, 4 May 2016 (diff | hist) . . (+14) . . Main Page
- 15:24, 4 May 2016 (diff | hist) . . (+194) . . SPAdes
- 15:20, 4 May 2016 (diff | hist) . . (+34) . . N SPAdes (Created page with "= Introduction = Pavel Pevzsner's")
- 14:54, 4 May 2016 (diff | hist) . . (+13) . . Main Page
- 16:23, 1 May 2016 (diff | hist) . . (+637) . . N Cd-hit (Created page with "=Introduction= CD-HIT is primarily a clustering program which, for input, takes fasta sequence files which are being envisioned as databases against which query sequence file...") (current)
- 14:12, 1 May 2016 (diff | hist) . . (+13) . . Main Page
- 17:08, 29 April 2016 (diff | hist) . . (+140) . . Srst2
- 17:05, 29 April 2016 (diff | hist) . . (+197) . . Srst2
- 16:20, 29 April 2016 (diff | hist) . . (+403) . . N Queue Manager Tips (Created page with "= Pipe a jobscript to '''qsub'''= echo -e 'date; sleep 2; date' | qsub -cwd -j y -V -S /bin/bash -q all.q -N pipetest This will send a string with the command date, followe...")
- 16:13, 29 April 2016 (diff | hist) . . (+473) . . Main Page
- 15:14, 29 April 2016 (diff | hist) . . (+73) . . Srst2
- 15:11, 29 April 2016 (diff | hist) . . (+800) . . Srst2
- 14:58, 29 April 2016 (diff | hist) . . (+108) . . Srst2
- 14:57, 29 April 2016 (diff | hist) . . (+3) . . Srst2
- 14:55, 29 April 2016 (diff | hist) . . (+81) . . Srst2
- 14:49, 29 April 2016 (diff | hist) . . (+151) . . Srst2
- 14:46, 29 April 2016 (diff | hist) . . (+82) . . Srst2
- 14:44, 29 April 2016 (diff | hist) . . (+7) . . Srst2
- 14:35, 29 April 2016 (diff | hist) . . (+27) . . Srst2
- 14:33, 29 April 2016 (diff | hist) . . (+68) . . Srst2
- 14:26, 29 April 2016 (diff | hist) . . (+69) . . Srst2
- 14:25, 29 April 2016 (diff | hist) . . (+185) . . Srst2
- 14:08, 29 April 2016 (diff | hist) . . (+157) . . Srst2
- 13:32, 29 April 2016 (diff | hist) . . (+491) . . Srst2
- 17:25, 28 April 2016 (diff | hist) . . (+48) . . Srst2
- 17:22, 28 April 2016 (diff | hist) . . (+459) . . Srst2
- 17:16, 28 April 2016 (diff | hist) . . (+138) . . Srst2
- 17:09, 28 April 2016 (diff | hist) . . (+228) . . Srst2
- 17:05, 28 April 2016 (diff | hist) . . (+70) . . Srst2
- 17:03, 28 April 2016 (diff | hist) . . (+2) . . Srst2
- 17:01, 28 April 2016 (diff | hist) . . (+442) . . Srst2
- 16:35, 28 April 2016 (diff | hist) . . (+68) . . Srst2
- 16:20, 28 April 2016 (diff | hist) . . (+489) . . Srst2
- 15:35, 28 April 2016 (diff | hist) . . (+82) . . Srst2
- 15:22, 28 April 2016 (diff | hist) . . (+255) . . Srst2
- 15:12, 28 April 2016 (diff | hist) . . (+88) . . Srst2
- 15:11, 28 April 2016 (diff | hist) . . (+290) . . Srst2
- 17:53, 27 April 2016 (diff | hist) . . (+202) . . Srst2
- 17:48, 27 April 2016 (diff | hist) . . (+172) . . Srst2
- 11:34, 21 April 2016 (diff | hist) . . (+299) . . Diamond
- 18:39, 20 April 2016 (diff | hist) . . (+189) . . Pyrad (current)
- 18:36, 20 April 2016 (diff | hist) . . (+184) . . Pyrad
- 18:22, 20 April 2016 (diff | hist) . . (+142) . . Pyrad
- 18:20, 20 April 2016 (diff | hist) . . (+3) . . Pyrad
- 18:17, 20 April 2016 (diff | hist) . . (+42) . . Pyrad
- 18:16, 20 April 2016 (diff | hist) . . (+70) . . Pyrad
- 18:11, 20 April 2016 (diff | hist) . . (+134) . . Pyrad
- 18:08, 20 April 2016 (diff | hist) . . (+2) . . Pyrad
- 18:07, 20 April 2016 (diff | hist) . . (+5) . . Pyrad
- 18:06, 20 April 2016 (diff | hist) . . (+135) . . Pyrad
- 18:04, 20 April 2016 (diff | hist) . . (0) . . Pyrad
- 18:03, 20 April 2016 (diff | hist) . . (+35) . . Pyrad
- 18:03, 20 April 2016 (diff | hist) . . (+49) . . Pyrad
- 18:02, 20 April 2016 (diff | hist) . . (+134) . . Pyrad
- 17:58, 20 April 2016 (diff | hist) . . (+547) . . Pyrad
- 17:08, 20 April 2016 (diff | hist) . . (+37) . . N Pyrad (Created page with " The go-to tutorial for this is at: *")
- 16:02, 20 April 2016 (diff | hist) . . (+12) . . Main Page
- 17:52, 19 April 2016 (diff | hist) . . (+432) . . Stacks
- 14:33, 19 April 2016 (diff | hist) . . (+3) . . Stacks
- 14:33, 19 April 2016 (diff | hist) . . (+2) . . Stacks
- 14:32, 19 April 2016 (diff | hist) . . (+330) . . Stacks
- 14:05, 19 April 2016 (diff | hist) . . (+2) . . Stacks
- 14:05, 19 April 2016 (diff | hist) . . (+1) . . Stacks
- 14:04, 19 April 2016 (diff | hist) . . (+2) . . Stacks
- 14:03, 19 April 2016 (diff | hist) . . (+1) . . Stacks
- 14:03, 19 April 2016 (diff | hist) . . (+195) . . Stacks
- 13:53, 19 April 2016 (diff | hist) . . (+34) . . Stacks
- 13:52, 19 April 2016 (diff | hist) . . (+88) . . Stacks
- 14:58, 18 April 2016 (diff | hist) . . (+302) . . N Stacks (Created page with "Dominant Radseq analysis software protocol by Julian Catchen. =Steps= * create database * ensure $STACKSROOTDIR/share/stacks/sql/my.cnf is set up properly * ensure modificat...")
- 14:40, 18 April 2016 (diff | hist) . . (+13) . . Main Page
- 17:02, 8 April 2016 (diff | hist) . . (+85) . . Synthetic Long reads (current)
- 16:55, 8 April 2016 (diff | hist) . . (0) . . N File:Biopipe.png (current)
- 16:34, 8 April 2016 (diff | hist) . . (-134) . . Synthetic Long reads
- 16:33, 8 April 2016 (diff | hist) . . (+137) . . Synthetic Long reads
- 16:24, 8 April 2016 (diff | hist) . . (+477) . . Galaxy Setup (current)
- 16:12, 8 April 2016 (diff | hist) . . (+10) . . Synthetic Long reads
- 16:01, 8 April 2016 (diff | hist) . . (+1,617) . . N Synthetic Long reads (Created page with "NGS reads are short in that they found in the 50-200 base-pair length scale. Longer reads are seen as more powerful, so there is a general tendency towards longer reads which...")
- 15:09, 8 April 2016 (diff | hist) . . (+39) . . Main Page
- 15:06, 8 April 2016 (diff | hist) . . (+10) . . Cluster Manual
- 12:43, 8 April 2016 (diff | hist) . . (0) . . N File:Welc.png (current)
- 12:19, 8 April 2016 (diff | hist) . . (+53) . . Python (current)
- 23:55, 7 April 2016 (diff | hist) . . (+10,887) . . N Cluster Manual (Created page with "=Introduction= This manual provides a brief introduction to the usage of St. Andrews’s bioinformatics cluster which consists of the frontend which we call marvin and its te...")
- 23:52, 7 April 2016 (diff | hist) . . (+19) . . Main Page
- 23:15, 7 April 2016 (diff | hist) . . (-69) . . Main Page
- 23:12, 7 April 2016 (diff | hist) . . (+371) . . N Galaxy Setup (Created page with "Galaxy is easy to set up as single user on a laptop, because it's most probably devoid of currently webservices. In other words, the Peronsal edition is easy. O install on mu...")
- 21:11, 7 April 2016 (diff | hist) . . (+20) . . CallSNPs.py
- 13:53, 7 April 2016 (diff | hist) . . (+31) . . Main Page
- 18:48, 6 April 2016 (diff | hist) . . (0) . . File:Callsnppipe.png (Rf uploaded a new version of File:Callsnppipe.png) (current)
- 18:46, 6 April 2016 (diff | hist) . . (+24) . . Velvet
- 18:43, 6 April 2016 (diff | hist) . . (0) . . N File:Intleaved.png (current)
- 18:32, 6 April 2016 (diff | hist) . . (+439) . . Velvet
- 18:28, 6 April 2016 (diff | hist) . . (+18) . . Velvet
- 16:26, 4 April 2016 (diff | hist) . . (+51) . . CallSNPs.py
- 11:26, 4 April 2016 (diff | hist) . . (+84) . . CallSNPs.py (→Stages)
- 11:25, 4 April 2016 (diff | hist) . . (+4) . . CallSNPs.py
- 11:24, 4 April 2016 (diff | hist) . . (+20) . . CallSNPs.py (→Stages)
- 11:21, 4 April 2016 (diff | hist) . . (0) . . N File:Callsnppipe.png
- 11:02, 4 April 2016 (diff | hist) . . (+3) . . CallSNPs.py
- 11:01, 4 April 2016 (diff | hist) . . (+64) . . CallSNPs.py (→Extract features with minimum coverage)
- 10:51, 4 April 2016 (diff | hist) . . (+43) . . CallSNPs.py
- 23:16, 3 April 2016 (diff | hist) . . (+70) . . CallSNPs.py (→Create fasta file from merged VCF file)
- 16:11, 3 April 2016 (diff | hist) . . (-12) . . CallSNPs.py (→Create fasta file from merged VCF file)
- 16:04, 3 April 2016 (diff | hist) . . (-34) . . CallSNPs.py
- 16:03, 3 April 2016 (diff | hist) . . (+176) . . CallSNPs.py (→9. Create fasta file from merged VCF file)
- 16:01, 3 April 2016 (diff | hist) . . (+25) . . CallSNPs.py (→9. Create fasta file from merged VCF file)
- 15:56, 3 April 2016 (diff | hist) . . (+227) . . CallSNPs.py
- 15:46, 3 April 2016 (diff | hist) . . (0) . . CallSNPs.py
- 15:45, 3 April 2016 (diff | hist) . . (+225) . . CallSNPs.py (→8. Merge VCF files)
- 15:38, 3 April 2016 (diff | hist) . . (+11) . . CallSNPs.py (→7. Filter recoded VCF file by quality expression)
- 15:37, 3 April 2016 (diff | hist) . . (+149) . . CallSNPs.py
- 15:25, 3 April 2016 (diff | hist) . . (+209) . . CallSNPs.py (→7. Filter recoded VCF file by quality expression)
- 15:23, 3 April 2016 (diff | hist) . . (+135) . . CallSNPs.py
- 15:12, 3 April 2016 (diff | hist) . . (+253) . . CallSNPs.py (→7. Merge recoded VCF files)
- 15:06, 3 April 2016 (diff | hist) . . (+179) . . CallSNPs.py
- 14:50, 3 April 2016 (diff | hist) . . (0) . . CallSNPs.py (→6. Merge vcf files to reflect common feature set)
- 14:50, 3 April 2016 (diff | hist) . . (+150) . . CallSNPs.py (→6. Merge vcf files to reflect common feature set)
- 14:38, 3 April 2016 (diff | hist) . . (+50) . . CallSNPs.py (→6. Merge vcf files to reflect common feature set)
- 14:21, 3 April 2016 (diff | hist) . . (+342) . . CallSNPs.py (→6. Merge vcf files)
- 14:12, 3 April 2016 (diff | hist) . . (+427) . . CallSNPs.py
- 14:02, 3 April 2016 (diff | hist) . . (-1) . . CallSNPs.py (→5. Intersect samples' features to find common features set)
- 13:05, 3 April 2016 (diff | hist) . . (-10) . . CallSNPs.py (→5. Intersect samples' fecture to find common features they all share)
- 13:05, 3 April 2016 (diff | hist) . . (+50) . . CallSNPs.py
- 13:03, 3 April 2016 (diff | hist) . . (+117) . . CallSNPs.py
- 13:00, 3 April 2016 (diff | hist) . . (+215) . . CallSNPs.py
- 12:24, 3 April 2016 (diff | hist) . . (+66) . . CallSNPs.py
- 23:35, 2 April 2016 (diff | hist) . . (+4) . . CallSNPs.py
- 23:26, 2 April 2016 (diff | hist) . . (+135) . . CallSNPs.py
- 23:21, 2 April 2016 (diff | hist) . . (0) . . CallSNPs.py
- 23:20, 2 April 2016 (diff | hist) . . (+131) . . CallSNPs.py
- 23:13, 2 April 2016 (diff | hist) . . (+282) . . CallSNPs.py
- 23:04, 2 April 2016 (diff | hist) . . (+130) . . CallSNPs.py (later)
- 22:18, 2 April 2016 (diff | hist) . . (+2) . . CallSNPs.py
- 22:16, 2 April 2016 (diff | hist) . . (0) . . CallSNPs.py
- 22:15, 2 April 2016 (diff | hist) . . (+8) . . CallSNPs.py
- 22:07, 2 April 2016 (diff | hist) . . (+14) . . CallSNPs.py
- 21:43, 2 April 2016 (diff | hist) . . (0) . . CallSNPs.py
- 14:50, 2 April 2016 (diff | hist) . . (+6) . . CallSNPs.py
- 14:50, 2 April 2016 (diff | hist) . . (+292) . . CallSNPs.py
- 18:24, 1 April 2016 (diff | hist) . . (+248) . . CallSNPs.py
- 17:50, 1 April 2016 (diff | hist) . . (+326) . . CallSNPs.py
- 17:16, 1 April 2016 (diff | hist) . . (+198) . . CallSNPs.py
- 17:10, 1 April 2016 (diff | hist) . . (+2) . . CallSNPs.py
- 16:53, 1 April 2016 (diff | hist) . . (+25) . . CallSNPs.py
- 16:50, 1 April 2016 (diff | hist) . . (-14) . . CallSNPs.py
- 16:49, 1 April 2016 (diff | hist) . . (-4) . . CallSNPs.py
- 16:48, 1 April 2016 (diff | hist) . . (+2) . . CallSNPs.py
- 16:48, 1 April 2016 (diff | hist) . . (+245) . . CallSNPs.py
- 16:41, 1 April 2016 (diff | hist) . . (+446) . . N CallSNPs.py (Created page with "This script is part of "script_tools" modules. It requires an alignment in the shape of the base reference sequence and the bam files of the short read aligned to that sequen...")
- 16:24, 1 April 2016 (diff | hist) . . (+37) . . Main Page
- 18:36, 31 March 2016 (diff | hist) . . (+157) . . N Bowtie2 (Created page with "= Introduction = = Install notes = * version 2.2.4 and upwards seem to use a new executable style whereby there is a principal bowtie2 executable and then") (current)
- 17:55, 31 March 2016 (diff | hist) . . (+14) . . Main Page
- 17:50, 31 March 2016 (diff | hist) . . (0) . . Srst2
- 17:46, 31 March 2016 (diff | hist) . . (+321) . . N Srst2 (Created page with "=introduction= This python based tool with two main dependencies (samtools and bowtie2) carries out mapping of short reads to detect overall three targets: 1) genes 2) allel...")
- 17:17, 31 March 2016 (diff | hist) . . (+12) . . Main Page
- 18:01, 30 March 2016 (diff | hist) . . (+503) . . BLAST
- 16:34, 30 March 2016 (diff | hist) . . (+458) . . N Velvet (Created page with "This is Daniel Zerbino and Ewan Birney's de-novo genome assembler and is one of the most widely used. It consists of two stages, a hashing stage invoked by the velveth progra...")
- 16:28, 30 March 2016 (diff | hist) . . (+13) . . Main Page
- 16:02, 29 March 2016 (diff | hist) . . (+728) . . N Python (Created page with "The issue with python on Marvin is that the simple "python" executable is not the bioinformatic python version. It's a version just for the system only. Instead, you have to...")
- 16:02, 29 March 2016 (diff | hist) . . (+13) . . Main Page
- 17:55, 24 March 2016 (diff | hist) . . (+356) . . Kallisto
- 19:51, 23 March 2016 (diff | hist) . . (0) . . Kallisto
- 19:50, 23 March 2016 (diff | hist) . . (+314) . . Kallisto
- 18:24, 23 March 2016 (diff | hist) . . (+20) . . Sra-tools
- 18:23, 23 March 2016 (diff | hist) . . (-127) . . Sra-tools
- 18:22, 23 March 2016 (diff | hist) . . (+176) . . Sra-tools
- 18:09, 23 March 2016 (diff | hist) . . (+278) . . N Kallisto (Created page with "It's the new (2015) way of calculating gene expression abundance from NGS short reads It calimms a large increase in speed by avoiding the normal alignment step =Using= ==...")
- 17:56, 23 March 2016 (diff | hist) . . (+7,574) . . Sra-tools
- 17:49, 23 March 2016 (diff | hist) . . (+5) . . Sra-tools
- 17:48, 23 March 2016 (diff | hist) . . (+468) . . N Sra-tools (Created page with "To load module load sra-tools the chief command for thsi tool box is fastq-dump, which downloads the SRA you are looking for Identifying the right SRA name is an issue, so...")
- 17:43, 23 March 2016 (diff | hist) . . (+31) . . Main Page
- 15:20, 8 February 2016 (diff | hist) . . (-2) . . Blast2go: b2g4pipe (→Installation and configuration) (current)
- 15:19, 8 February 2016 (diff | hist) . . (-231) . . Blast2go: b2g4pipe (→databases)
- 15:13, 8 February 2016 (diff | hist) . . (-74) . . Blast2go: b2g4pipe
- 15:11, 8 February 2016 (diff | hist) . . (+1,054) . . Blast2go: b2g4pipe
- 14:58, 8 February 2016 (diff | hist) . . (+442) . . N Blast2go: b2g4pipe (Created page with "Blast2go is the gene ontology annotation program for eukaryotes. Some time after 2012, it became commercialised, although the free usage of early version is still permitted....")
- 14:55, 8 February 2016 (diff | hist) . . (+25) . . Main Page
- 13:45, 8 February 2016 (diff | hist) . . (+206) . . N Diamond (Created page with "This is very fast alternative to the blastx program. This page contains some details about the program == key points made== * Describes blastx as the "gold standard" * high...")
- 12:21, 8 February 2016 (diff | hist) . . (+92) . . Main Page
- 19:22, 5 February 2016 (diff | hist) . . (+1) . . BLAST
- 19:22, 5 February 2016 (diff | hist) . . (+1,394) . . N BLAST (Created page with "This is probably the best known of all bioinformatics applications, and consequently has various different aspects to it. =mpiBLAST= This version which stopped development i...")
- 17:18, 1 February 2016 (diff | hist) . . (0) . . Blast
- 17:17, 1 February 2016 (diff | hist) . . (+221) . . Blast
- 15:59, 1 February 2016 (diff | hist) . . (+15) . . Blast
- 15:46, 1 February 2016 (diff | hist) . . (0) . . Blast
- 15:07, 1 February 2016 (diff | hist) . . (+301) . . N Blast (Created page with "=Introduction= The workhorse of bioinformatics, some tips on usgae, and (mostly) how to speed it up = Benchmark Exercises = == Transcriptome Panda Blood == * 92600 transcri...")
- 19:18, 19 January 2016 (diff | hist) . . (+17) . . Main Page
- 19:17, 19 January 2016 (diff | hist) . . (-19) . . STAR BEAST (current)
- 19:16, 19 January 2016 (diff | hist) . . (-6,960) . . STAR BEAST
- 19:07, 19 January 2016 (diff | hist) . . (+22,232) . . N STAR BEAST (Created page with " =Introduction= Bayesian Inference of Species Trees from Multilocus Data using *BEAST, Alexei J Drummond, Walter Xie and Joseph Heled April 13, 2012 Provides joint inferenc...")
- 18:54, 19 January 2016 (diff | hist) . . (+40) . . Main Page
- 18:52, 19 January 2016 (diff | hist) . . (-536) . . Main Page (Replaced content with "Placeholder wiki == Protocols == * Trinity_Protocol")
- 20:29, 18 January 2016 (diff | hist) . . (-90) . . Globus gridftp (current)
- 20:27, 18 January 2016 (diff | hist) . . (+59) . . Globus gridftp
- 20:22, 18 January 2016 (diff | hist) . . (+2,155) . . N Globus gridftp (Created page with "=Introduction= * Well-established secure data distribution system designed with research in mind * Ofrece un entorno parecido a FTP pero más seguro (hay dos niveles de segur...")
- 18:19, 18 January 2016 (diff | hist) . . (+21,371) . . Trinity Protocol
- 18:08, 18 January 2016 (diff | hist) . . (+826) . . N Trinity Protocol (Created page with "This is the Trinity protocol for assembling transcriptomes ==Timing== Steps 1–3, collection of RNA-seq data: ~10 min Steps 4–7, Trinity de novo transcriptome assembly...")
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