User contributions
(newest | oldest) View (newer 50 | older 50) (20 | 50 | 100 | 250 | 500)
- 16:15, 20 February 2016 (diff | hist) . . (+2,731) . . N 9.3 SNP calling using varscan (Created page with "First, you need to sort the '''SAM''' file, and then generate a so-called '''pileup file''', which describes how the reads align to the reference genome positi...")
- 16:07, 20 February 2016 (diff | hist) . . (+31) . . 9.2 Read mapping using bwa (current)
- 16:06, 20 February 2016 (diff | hist) . . (+897) . . 9.2 Read mapping using bwa
- 16:03, 20 February 2016 (diff | hist) . . (-23) . . 9.2 Read mapping using bwa
- 15:59, 20 February 2016 (diff | hist) . . (-3) . . 9.1 Genome indexing for bwa (current)
- 15:58, 20 February 2016 (diff | hist) . . (-2) . . 9.1 Genome indexing for bwa
- 15:58, 20 February 2016 (diff | hist) . . (-3) . . 9.1 Genome indexing for bwa
- 15:57, 20 February 2016 (diff | hist) . . (+15) . . 9.1 Genome indexing for bwa
- 15:49, 20 February 2016 (diff | hist) . . (+766) . . N 9.2 Read mapping using bwa (Created page with "Read mapping with '''bwa''' is peculiar in which it requires two steps: in the first, bwa produces the mapping using an internal format (called sai fo...")
- 15:48, 20 February 2016 (diff | hist) . . (+1,005) . . 9.1 Genome indexing for bwa
- 15:47, 20 February 2016 (diff | hist) . . (+1,225) . . N 9.1 Genome indexing for bwa (Created page with "Let’s first look at the bwa options: $ module load bwa/0.7.12 $ bwa The '''bwa''' suite provides a number of commands for various steps of the alignment ...")
- 15:44, 20 February 2016 (diff | hist) . . (+1,429) . . N 9. Using bwa for read mapping and SNP calling (Created page with "Another popular mapping tool is '''bwa''', which many prefer to '''bowtie'''. As an optional exercise, you will learn how to perform the '''bwa mapping''', but y...") (current)
- 15:32, 20 February 2016 (diff | hist) . . (0) . . RNA Seq on HPC (current)
- 10:58, 18 February 2016 (diff | hist) . . (-68) . . 6.3 Transcriptome reconstruction and expression using cufflinks (current)
- 10:48, 18 February 2016 (diff | hist) . . (+1,258) . . 6.4 Differential Expression using cuffdiff (current)
- 10:45, 18 February 2016 (diff | hist) . . (+2,065) . . 6.4 Differential Expression using cuffdiff
- 10:41, 18 February 2016 (diff | hist) . . (+493) . . 6.4 Differential Expression using cuffdiff
- 10:38, 18 February 2016 (diff | hist) . . (+3) . . 6.4 Differential Expression using cuffdiff
- 10:37, 18 February 2016 (diff | hist) . . (+1,311) . . N 6.4 Differential Expression using cuffdiff (Created page with "One of the stand-alone tools that are part of the '''cufflinks''' package, and that performs differential expression estimation, is '''cuffdiff'''. You can use this tool to c...")
- 17:33, 15 February 2016 (diff | hist) . . (-2) . . 6.3 Transcriptome reconstruction and expression using cufflinks
- 17:33, 15 February 2016 (diff | hist) . . (+13) . . 6.3 Transcriptome reconstruction and expression using cufflinks
- 17:31, 15 February 2016 (diff | hist) . . (+1,130) . . 6.3 Transcriptome reconstruction and expression using cufflinks
- 17:18, 15 February 2016 (diff | hist) . . (-3) . . 6.3 Transcriptome reconstruction and expression using cufflinks
- 17:17, 15 February 2016 (diff | hist) . . (+2,572) . . 6.3 Transcriptome reconstruction and expression using cufflinks
- 17:10, 15 February 2016 (diff | hist) . . (+1,217) . . 6.3 Transcriptome reconstruction and expression using cufflinks
- 17:08, 15 February 2016 (diff | hist) . . (+244) . . 6.3 Transcriptome reconstruction and expression using cufflinks
- 17:05, 15 February 2016 (diff | hist) . . (+4) . . 6.3 Transcriptome reconstruction and expression using cufflinks
- 17:05, 15 February 2016 (diff | hist) . . (+1,051) . . 6.3 Transcriptome reconstruction and expression using cufflinks
- 17:03, 15 February 2016 (diff | hist) . . (+3) . . 6.3 Transcriptome reconstruction and expression using cufflinks
- 17:03, 15 February 2016 (diff | hist) . . (+1) . . 6.3 Transcriptome reconstruction and expression using cufflinks
- 17:02, 15 February 2016 (diff | hist) . . (+50) . . 6.3 Transcriptome reconstruction and expression using cufflinks
- 17:02, 15 February 2016 (diff | hist) . . (+416) . . 6.3 Transcriptome reconstruction and expression using cufflinks
- 16:59, 15 February 2016 (diff | hist) . . (+587) . . 6.3 Transcriptome reconstruction and expression using cufflinks
- 16:02, 12 February 2016 (diff | hist) . . (-2) . . 6.3 Transcriptome reconstruction and expression using cufflinks
- 16:02, 12 February 2016 (diff | hist) . . (+1,155) . . N 6.3 Transcriptome reconstruction and expression using cufflinks (Created page with "There are a number of tools that perform reconstruction of the transcriptome and for this workshop you are going to use '''cufflinks''', which can do transcripto...")
- 15:55, 12 February 2016 (diff | hist) . . (-548) . . 6.2 Read mapping using tophat (current)
- 15:55, 12 February 2016 (diff | hist) . . (+566) . . 6.2 Read mapping using tophat
- 15:53, 12 February 2016 (diff | hist) . . (+19) . . 6.1 Genome indexing for bowtie
- 18:49, 4 February 2016 (diff | hist) . . (+4) . . 6.2 Read mapping using tophat
- 13:55, 4 February 2016 (diff | hist) . . (+432) . . 6.2 Read mapping using tophat
- 13:53, 4 February 2016 (diff | hist) . . (-1) . . 6.2 Read mapping using tophat
- 13:53, 4 February 2016 (diff | hist) . . (+413) . . 6.2 Read mapping using tophat
- 13:50, 4 February 2016 (diff | hist) . . (+353) . . 6.2 Read mapping using tophat
- 13:48, 4 February 2016 (diff | hist) . . (+18) . . 6.2 Read mapping using tophat
- 13:47, 4 February 2016 (diff | hist) . . (+431) . . 6.2 Read mapping using tophat
- 13:46, 4 February 2016 (diff | hist) . . (+1,127) . . 6.2 Read mapping using tophat
- 13:42, 4 February 2016 (diff | hist) . . (-148) . . 6.2 Read mapping using tophat
- 13:39, 4 February 2016 (diff | hist) . . (+727) . . 6.2 Read mapping using tophat
- 13:36, 4 February 2016 (diff | hist) . . (+2) . . 6.2 Read mapping using tophat
- 13:36, 4 February 2016 (diff | hist) . . (+209) . . 6.2 Read mapping using tophat
(newest | oldest) View (newer 50 | older 50) (20 | 50 | 100 | 250 | 500)
