Anders2013: Revision history

1 July 2014

• curprev 12:3612:36, 1 July 2014‎ Brb talk contribs‎ 35,594 bytes +90‎ →‎Tophat options

24 June 2014

• curprev 12:0612:06, 24 June 2014‎ Brb talk contribs‎ 35,504 bytes +30‎ →‎Check Coverage from bam file
• curprev 11:0211:02, 24 June 2014‎ Brb talk contribs‎ 35,474 bytes +151‎ →‎Output from console

23 June 2014

• curprev 10:2510:25, 23 June 2014‎ Brb talk contribs‎ 35,323 bytes −105‎ →‎Tophat options
• curprev 10:2410:24, 23 June 2014‎ Brb talk contribs‎ 35,428 bytes −1‎ →‎Tophat options
• curprev 10:2310:23, 23 June 2014‎ Brb talk contribs‎ 35,429 bytes +807‎ →‎Tophat options
• curprev 10:1910:19, 23 June 2014‎ Brb talk contribs‎ 34,622 bytes +21‎ →‎Tophat options
• curprev 10:1810:18, 23 June 2014‎ Brb talk contribs‎ 34,601 bytes +409‎ →‎Align the reads to the reference genome using tophat2 (fastq -> bam, bed)

9 June 2014

• curprev 10:2210:22, 9 June 2014‎ Brb talk contribs‎ 34,192 bytes +36‎ →‎ENCODE
• curprev 09:5709:57, 9 June 2014‎ Brb talk contribs‎ 34,156 bytes +33‎ →‎Galaxy
• curprev 09:4809:48, 9 June 2014‎ Brb talk contribs‎ 34,123 bytes +6‎ →‎Output from console
• curprev 09:4509:45, 9 June 2014‎ Brb talk contribs‎ 34,117 bytes +121‎ →‎Count reads using htseq-count (sam -> count)

4 June 2014

• curprev 11:2711:27, 4 June 2014‎ Brb talk contribs‎ 33,996 bytes +434‎ →‎Cufflink -> Cuffcompare -> Cuffdiff
• curprev 11:1411:14, 4 June 2014‎ Brb talk contribs‎ 33,562 bytes +135‎ →‎Other RNA-Seq tools
• curprev 11:0911:09, 4 June 2014‎ Brb talk contribs‎ 33,427 bytes +146‎ →‎Download GTF (gene transfer format) file (for Tophat)

3 June 2014

• curprev 16:2616:26, 3 June 2014‎ Brb talk contribs‎ 33,281 bytes +52‎ →‎Download GTF (gene transfer format) file (for Tophat)
• curprev 16:2516:25, 3 June 2014‎ Brb talk contribs‎ 33,229 bytes +110‎ →‎Download GTF (gene transfer format) file (for Tophat)

23 May 2014

• curprev 22:2522:25, 23 May 2014‎ Brb talk contribs‎ 33,119 bytes +12‎ →‎Preprocess reference FASTA files into an index (fasta -> bt2)

15 May 2014

• curprev 10:0110:01, 15 May 2014‎ Brb talk contribs‎ 33,107 bytes +53‎ →‎Pipeline
• curprev 09:5809:58, 15 May 2014‎ Brb talk contribs‎ 33,054 bytes +200‎ No edit summary

9 May 2014

• curprev 09:3209:32, 9 May 2014‎ Brb talk contribs‎ 32,854 bytes +9‎ →‎Change PATH variable

25 April 2014

• curprev 16:0016:00, 25 April 2014‎ Brb talk contribs‎ 32,845 bytes +184‎ →‎Required tools
• curprev 15:5615:56, 25 April 2014‎ Brb talk contribs‎ 32,661 bytes +361‎ →‎Access quality control through ShortRead or FastQC

22 April 2014

• curprev 10:1010:10, 22 April 2014‎ Brb talk contribs‎ 32,300 bytes −11‎ →‎Installation
• curprev 10:0710:07, 22 April 2014‎ Brb talk contribs‎ 32,311 bytes +14‎ →‎Installation
• curprev 10:0610:06, 22 April 2014‎ Brb talk contribs‎ 32,297 bytes +18‎ →‎Installation
• curprev 08:5908:59, 22 April 2014‎ Brb talk contribs‎ 32,279 bytes −105‎ →‎Installation
• curprev 08:5808:58, 22 April 2014‎ Brb talk contribs‎ 32,384 bytes −28‎ →‎Installation
• curprev 08:5708:57, 22 April 2014‎ Brb talk contribs‎ 32,412 bytes −6‎ →‎Installation
• curprev 08:5508:55, 22 April 2014‎ Brb talk contribs‎ 32,418 bytes −58‎ →‎Installation

21 April 2014

• curprev 16:4716:47, 21 April 2014‎ Brb talk contribs‎ 32,476 bytes −1,495‎ →‎Installation
• curprev 16:3316:33, 21 April 2014‎ Brb talk contribs‎ 33,971 bytes +162‎ →‎Installation
• curprev 15:3615:36, 21 April 2014‎ Brb talk contribs‎ 33,809 bytes +153‎ →‎Installation
• curprev 15:2615:26, 21 April 2014‎ Brb talk contribs‎ 33,656 bytes +68‎ →‎Installation
• curprev 15:1715:17, 21 April 2014‎ Brb talk contribs‎ 33,588 bytes +35‎ →‎Change PATH variable
• curprev 15:1515:15, 21 April 2014‎ Brb talk contribs‎ 33,553 bytes +182‎ →‎Installation
• curprev 15:0715:07, 21 April 2014‎ Brb talk contribs‎ 33,371 bytes +890‎ →‎Installation
• curprev 14:4714:47, 21 April 2014‎ Brb talk contribs‎ 32,481 bytes +181‎ →‎Count reads using htseq-count (sam -> count)
• curprev 14:4414:44, 21 April 2014‎ Brb talk contribs‎ 32,300 bytes −6‎ →‎Installation
• curprev 14:4214:42, 21 April 2014‎ Brb talk contribs‎ 32,306 bytes +425‎ →‎Required tools
• curprev 13:5713:57, 21 April 2014‎ Brb talk contribs‎ 31,881 bytes +7‎ →‎Required tools
• curprev 10:3810:38, 21 April 2014‎ Brb talk contribs‎ 31,874 bytes +82‎ →‎Organize, sort and index the BAM files and create SAM files (bam -> sam)
• curprev 10:3710:37, 21 April 2014‎ Brb talk contribs‎ 31,792 bytes +2,032‎ →‎Align the reads to the reference genome using tophat2 (fastq -> bam, bed)

15 April 2014

• curprev 10:5910:59, 15 April 2014‎ Brb talk contribs‎ 29,760 bytes +55‎ →‎Galaxy
• curprev 10:5310:53, 15 April 2014‎ Brb talk contribs‎ 29,705 bytes +200‎ →‎GEO
• curprev 10:5110:51, 15 April 2014‎ Brb talk contribs‎ 29,505 bytes +63‎ →‎GEO
• curprev 10:4910:49, 15 April 2014‎ Brb talk contribs‎ 29,442 bytes +151‎ →‎GEO

14 April 2014

• curprev 08:5808:58, 14 April 2014‎ Brb talk contribs‎ 29,291 bytes +52‎ →‎Required tools

9 April 2014

• curprev 12:5212:52, 9 April 2014‎ Brb talk contribs‎ 29,239 bytes +28‎ →‎GEO
• curprev 12:5112:51, 9 April 2014‎ Brb talk contribs‎ 29,211 bytes +153‎ →‎GEO
• curprev 12:4012:40, 9 April 2014‎ Brb talk contribs‎ 29,058 bytes +325‎ No edit summary
• curprev 11:3911:39, 9 April 2014‎ Brb talk contribs‎ 28,733 bytes +67‎ →‎Other RNA-Seq tools
• curprev 11:3011:30, 9 April 2014‎ Brb talk contribs‎ 28,666 bytes +87‎ →‎Inspect alignments with IGV
• curprev 11:2711:27, 9 April 2014‎ Brb talk contribs‎ 28,579 bytes +136‎ →‎Inspect alignments with IGV
• curprev 11:0811:08, 9 April 2014‎ Brb talk contribs‎ 28,443 bytes +459‎ →‎Inspect alignments with IGV
• curprev 11:0111:01, 9 April 2014‎ Brb talk contribs‎ 27,984 bytes −5‎ →‎Inspect alignments with IGV
• curprev 11:0011:00, 9 April 2014‎ Brb talk contribs‎ 27,989 bytes +840‎ →‎Inspect alignments with IGV

2 April 2014

• curprev 13:1613:16, 2 April 2014‎ Brb talk contribs‎ 27,149 bytes +11‎ →‎Preprocess reference FASTA files into an index (fasta -> bt2)
• curprev 13:1313:13, 2 April 2014‎ Brb talk contribs‎ 27,138 bytes +219‎ →‎Preprocess reference FASTA files into an index (fasta -> bt2)
• curprev 13:0513:05, 2 April 2014‎ Brb talk contribs‎ 26,919 bytes +1,605‎ →‎Download reference genome
• curprev 09:5809:58, 2 April 2014‎ Brb talk contribs‎ 25,314 bytes +45‎ →‎GEO

1 April 2014

• curprev 09:3009:30, 1 April 2014‎ Brb talk contribs‎ 25,269 bytes +368‎ →‎Human BodyMap 2.0 data from Illumina

31 March 2014

• curprev 15:0415:04, 31 March 2014‎ Brb talk contribs‎ 24,901 bytes 0‎ →‎Human BodyMap 2.0 data from Illumina
• curprev 15:0315:03, 31 March 2014‎ Brb talk contribs‎ 24,901 bytes 0‎ →‎Human BodyMap 2.0 data from Illumina
• curprev 15:0115:01, 31 March 2014‎ Brb talk contribs‎ 24,901 bytes −59‎ →‎Human BodyMap 2.0 data from Illumina
• curprev 14:4714:47, 31 March 2014‎ Brb talk contribs‎ 24,960 bytes +388‎ →‎Human BodyMap 2.0 data from Illumina
• curprev 14:1514:15, 31 March 2014‎ Brb talk contribs‎ 24,572 bytes −10‎ →‎The PATH variable
• curprev 14:1014:10, 31 March 2014‎ Brb talk contribs‎ 24,582 bytes +35‎ →‎Galaxy
• curprev 14:0814:08, 31 March 2014‎ Brb talk contribs‎ 24,547 bytes +148‎ →‎Galaxy
• curprev 14:0014:00, 31 March 2014‎ Brb talk contribs‎ 24,399 bytes +70‎ →‎Other RNA-Seq data

30 March 2014

• curprev 18:3018:30, 30 March 2014‎ Brb talk contribs‎ 24,329 bytes +123‎ →‎Other RNA-Seq data
• curprev 18:2518:25, 30 March 2014‎ Brb talk contribs‎ 24,206 bytes −52‎ →‎Other RNA-Seq data
• curprev 17:0617:06, 30 March 2014‎ Brb talk contribs‎ 24,258 bytes +110‎ →‎Other RNA-Seq data

28 March 2014

• curprev 16:2016:20, 28 March 2014‎ Brb talk contribs‎ 24,148 bytes +360‎ →‎Galaxy

27 March 2014

• curprev 16:0516:05, 27 March 2014‎ Brb talk contribs‎ 23,788 bytes +198‎ →‎Galaxy
• curprev 09:4309:43, 27 March 2014‎ Brb talk contribs‎ 23,590 bytes +141‎ →‎The PATH variable
• curprev 09:3609:36, 27 March 2014‎ Brb talk contribs‎ 23,449 bytes +254‎ →‎Galaxy

25 March 2014

• curprev 20:4220:42, 25 March 2014‎ Brb talk contribs‎ 23,195 bytes +171‎ →‎Galaxy
• curprev 19:4919:49, 25 March 2014‎ Brb talk contribs‎ 23,024 bytes +351‎ →‎Other RNA-Seq tools
• curprev 19:3419:34, 25 March 2014‎ Brb talk contribs‎ 22,673 bytes +83‎ No edit summary

21 March 2014

• curprev 11:2011:20, 21 March 2014‎ Brb talk contribs‎ 22,590 bytes +39‎ →‎The PATH variable
• curprev 11:1811:18, 21 March 2014‎ Brb talk contribs‎ 22,551 bytes +114‎ →‎Organize, sort and index the BAM files and create SAM files (bam -> sam)
• curprev 11:1511:15, 21 March 2014‎ Brb talk contribs‎ 22,437 bytes +271‎ →‎Organize, sort and index the BAM files and create SAM files (bam -> sam)
• curprev 11:0711:07, 21 March 2014‎ Brb talk contribs‎ 22,166 bytes +89‎ →‎Organize, sort and index the BAM files and create SAM files (bam -> sam)
• curprev 10:5210:52, 21 March 2014‎ Brb talk contribs‎ 22,077 bytes +103‎ →‎Organize, sort and index the BAM files and create SAM files (bam -> sam)
• curprev 10:3310:33, 21 March 2014‎ Brb talk contribs‎ 21,974 bytes +223‎ →‎Organize, sort and index the BAM files and create SAM files (bam -> sam)

20 March 2014

• curprev 11:4711:47, 20 March 2014‎ Brb talk contribs‎ 21,751 bytes +35‎ →‎Required tools

19 March 2014

• curprev 13:3613:36, 19 March 2014‎ Brb talk contribs‎ 21,716 bytes −1‎ →‎Required tools
• curprev 09:2509:25, 19 March 2014‎ Brb talk contribs‎ 21,717 bytes +28‎ No edit summary

18 March 2014

• curprev 21:0321:03, 18 March 2014‎ Brb talk contribs‎ 21,689 bytes −115‎ →‎Required tools
• curprev 21:0121:01, 18 March 2014‎ Brb talk contribs‎ 21,804 bytes +88‎ →‎Required tools
• curprev 15:5115:51, 18 March 2014‎ Brb talk contribs‎ 21,716 bytes +322‎ →‎Data directory
• curprev 15:4815:48, 18 March 2014‎ Brb talk contribs‎ 21,394 bytes +161‎ No edit summary

12 March 2014

• curprev 08:5508:55, 12 March 2014‎ Brb talk contribs‎ 21,233 bytes +82‎ →‎Pipeline
• curprev 08:5308:53, 12 March 2014‎ Brb talk contribs‎ 21,151 bytes +61‎ →‎Data directory
• curprev 08:5208:52, 12 March 2014‎ Brb talk contribs‎ 21,090 bytes −2‎ →‎Data directory
• curprev 08:5208:52, 12 March 2014‎ Brb talk contribs‎ 21,092 bytes +63‎ →‎Data directory
• curprev 08:5008:50, 12 March 2014‎ Brb talk contribs‎ 21,029 bytes +156‎ →‎Data directory

8 March 2014

• curprev 23:4323:43, 8 March 2014‎ Brb talk contribs‎ 20,873 bytes +14,247‎ →‎Pipeline
• curprev 23:2723:27, 8 March 2014‎ Brb talk contribs‎ 6,626 bytes +6,626‎ Created page with "The data is used in the paper "Count-based differential ....." by [http://www.nature.com/nprot/journal/v8/n9/abs/nprot.2013.099.html Anders et al 2013]. = Required tools = Th..."