User contributions
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- 15:48, 1 April 2016 (diff | hist) . . (+245) . . CallSNPs.py
- 15:41, 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...")
- 15:24, 1 April 2016 (diff | hist) . . (+37) . . Main Page
- 17:36, 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)
- 16:55, 31 March 2016 (diff | hist) . . (+14) . . Main Page
- 16:50, 31 March 2016 (diff | hist) . . (0) . . Srst2
- 16:46, 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...")
- 16:17, 31 March 2016 (diff | hist) . . (+12) . . Main Page
- 17:01, 30 March 2016 (diff | hist) . . (+503) . . BLAST
- 15:34, 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...")
- 15:28, 30 March 2016 (diff | hist) . . (+13) . . Main Page
- 15:02, 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...")
- 15:02, 29 March 2016 (diff | hist) . . (+13) . . Main Page
- 16:55, 24 March 2016 (diff | hist) . . (+356) . . Kallisto
- 18:51, 23 March 2016 (diff | hist) . . (0) . . Kallisto
- 18:50, 23 March 2016 (diff | hist) . . (+314) . . Kallisto
- 17:24, 23 March 2016 (diff | hist) . . (+20) . . Sra-tools
- 17:23, 23 March 2016 (diff | hist) . . (-127) . . Sra-tools
- 17:22, 23 March 2016 (diff | hist) . . (+176) . . Sra-tools
- 17:09, 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= ==...")
- 16:56, 23 March 2016 (diff | hist) . . (+7,574) . . Sra-tools
- 16:49, 23 March 2016 (diff | hist) . . (+5) . . Sra-tools
- 16:48, 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...")
- 16:43, 23 March 2016 (diff | hist) . . (+31) . . Main Page
- 14:20, 8 February 2016 (diff | hist) . . (-2) . . Blast2go: b2g4pipe (→Installation and configuration) (current)
- 14:19, 8 February 2016 (diff | hist) . . (-231) . . Blast2go: b2g4pipe (→databases)
- 14:13, 8 February 2016 (diff | hist) . . (-74) . . Blast2go: b2g4pipe
- 14:11, 8 February 2016 (diff | hist) . . (+1,054) . . Blast2go: b2g4pipe
- 13:58, 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....")
- 13:55, 8 February 2016 (diff | hist) . . (+25) . . Main Page
- 12:45, 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...")
- 11:21, 8 February 2016 (diff | hist) . . (+92) . . Main Page
- 18:22, 5 February 2016 (diff | hist) . . (+1) . . BLAST
- 18:22, 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...")
- 16:18, 1 February 2016 (diff | hist) . . (0) . . Blast
- 16:17, 1 February 2016 (diff | hist) . . (+221) . . Blast
- 14:59, 1 February 2016 (diff | hist) . . (+15) . . Blast
- 14:46, 1 February 2016 (diff | hist) . . (0) . . Blast
- 14:07, 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...")
- 18:18, 19 January 2016 (diff | hist) . . (+17) . . Main Page
- 18:17, 19 January 2016 (diff | hist) . . (-19) . . STAR BEAST (current)
- 18:16, 19 January 2016 (diff | hist) . . (-6,960) . . STAR BEAST
- 18:07, 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...")
- 17:54, 19 January 2016 (diff | hist) . . (+40) . . Main Page
- 17:52, 19 January 2016 (diff | hist) . . (-536) . . Main Page (Replaced content with "Placeholder wiki == Protocols == * Trinity_Protocol")
- 19:29, 18 January 2016 (diff | hist) . . (-90) . . Globus gridftp (current)
- 19:27, 18 January 2016 (diff | hist) . . (+59) . . Globus gridftp
- 19:22, 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...")
- 17:19, 18 January 2016 (diff | hist) . . (+21,371) . . Trinity Protocol
- 17:08, 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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