User contributions
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- 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
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