Anders2013: Revision history

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curprev 12:3912:39, 24 February 2016‎ Brb talk contribs‎ 84,013 bytes +610‎ →‎sam/bam, "samtools view" and Rsamtools

curprev 20:5420:54, 23 February 2016‎ Brb talk contribs‎ 83,403 bytes +319‎ →‎sam, bam and samtools view
curprev 20:3620:36, 23 February 2016‎ Brb talk contribs‎ 83,084 bytes +265‎ →‎Organize, sort and index the BAM files and create SAM files (bam -> sam)
curprev 20:2820:28, 23 February 2016‎ Brb talk contribs‎ 82,819 bytes +173‎ →‎sam, bam
curprev 12:4312:43, 23 February 2016‎ Brb talk contribs‎ 82,646 bytes +413‎ →‎fasta

curprev 12:3412:34, 15 January 2016‎ Brb talk contribs‎ 82,233 bytes +380‎ →‎TCGA

curprev 14:3514:35, 31 December 2015‎ Brb talk contribs‎ 81,853 bytes +180‎ →‎GEO

curprev 14:2214:22, 7 December 2015‎ Brb talk contribs‎ 81,673 bytes +96‎ →‎GEO

curprev 11:3711:37, 10 November 2015‎ Brb talk contribs‎ 81,577 bytes +81,250‎ No edit summary
curprev 11:3311:33, 10 November 2015‎ Brb talk contribs‎ 327 bytes −80,979‎ Replaced content with "== ReCount == * [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3229291/ ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets] * http://bowtie-b..."

curprev 16:0816:08, 28 October 2015‎ Brb talk contribs‎ 81,306 bytes −143‎ →‎Normalization
curprev 16:0516:05, 28 October 2015‎ Brb talk contribs‎ 81,449 bytes +143‎ →‎Normalization
curprev 16:0116:01, 28 October 2015‎ Brb talk contribs‎ 81,306 bytes +176‎ →‎Normalization

curprev 18:4518:45, 19 September 2015‎ Brb talk contribs‎ 81,130 bytes +97‎ →‎TCGA

curprev 15:5115:51, 14 September 2015‎ Brb talk contribs‎ 79,136 bytes +15‎ →‎Cufflink -> Cuffcompare -> Cuffdiff

curprev 12:0712:07, 21 August 2015‎ Brb talk contribs‎ 79,121 bytes +43‎ →‎File Format

curprev 16:1516:15, 19 August 2015‎ Brb talk contribs‎ 79,078 bytes +347‎ →‎Tophat options
curprev 16:0316:03, 19 August 2015‎ Brb talk contribs‎ 78,731 bytes +15‎ →‎gff/gtf
curprev 16:0016:00, 19 August 2015‎ Brb talk contribs‎ 78,716 bytes +114‎ →‎gff/gtf
curprev 15:5315:53, 19 August 2015‎ Brb talk contribs‎ 78,602 bytes +96‎ →‎gff/gtf

curprev 15:5715:57, 18 August 2015‎ Brb talk contribs‎ 78,506 bytes +35‎ →‎gff/gtf

curprev 14:3814:38, 17 August 2015‎ Brb talk contribs‎ 78,471 bytes +366‎ →‎gff/gtf

curprev 10:1510:15, 10 August 2015‎ Brb talk contribs‎ 78,105 bytes +63‎ →‎sam, bam
curprev 09:4309:43, 10 August 2015‎ Brb talk contribs‎ 78,042 bytes +41‎ →‎bed

curprev 09:4609:46, 7 August 2015‎ Brb talk contribs‎ 78,001 bytes +16‎ →‎sam, bam
curprev 09:4509:45, 7 August 2015‎ Brb talk contribs‎ 77,985 bytes +185‎ →‎sam, bam
curprev 09:2409:24, 7 August 2015‎ Brb talk contribs‎ 77,800 bytes +104‎ →‎File Format

curprev 15:4615:46, 4 August 2015‎ Brb talk contribs‎ 77,696 bytes +986‎ →‎gff/gtf
curprev 15:1915:19, 4 August 2015‎ Brb talk contribs‎ 76,710 bytes +252‎ →‎Tophat options
curprev 15:1615:16, 4 August 2015‎ Brb talk contribs‎ 76,458 bytes +235‎ →‎Tophat options
curprev 14:5714:57, 4 August 2015‎ Brb talk contribs‎ 76,223 bytes +104‎ →‎Some lessons

curprev 09:1809:18, 30 July 2015‎ Brb talk contribs‎ 76,119 bytes +47‎ →‎TCGA

curprev 15:1515:15, 23 July 2015‎ Brb talk contribs‎ 76,072 bytes +43‎ →‎gff/gtf
curprev 15:0415:04, 23 July 2015‎ Brb talk contribs‎ 76,029 bytes +135‎ →‎gff/gtf

curprev 11:1211:12, 1 July 2015‎ Brb talk contribs‎ 75,091 bytes +141‎ →‎SRA data linked from QuickNGS
curprev 11:1011:10, 1 July 2015‎ Brb talk contribs‎ 74,950 bytes +144‎ →‎Other RNA-Seq data

curprev 13:1113:11, 11 June 2015‎ Brb talk contribs‎ 74,806 bytes +534‎ →‎Launch

curprev 10:5210:52, 28 May 2015‎ Brb talk contribs‎ 74,272 bytes +107‎ →‎Some lessons
curprev 10:4810:48, 28 May 2015‎ Brb talk contribs‎ 74,165 bytes 0‎ →‎Some lessons
curprev 10:4810:48, 28 May 2015‎ Brb talk contribs‎ 74,165 bytes −8‎ →‎Some lessons
curprev 10:4610:46, 28 May 2015‎ Brb talk contribs‎ 74,173 bytes +877‎ →‎FAQs for Tophat

curprev 09:5909:59, 27 May 2015‎ Brb talk contribs‎ 73,296 bytes +57‎ →‎FAQs for Tophat
curprev 08:5308:53, 27 May 2015‎ Brb talk contribs‎ 73,239 bytes +160‎ →‎FAQs for Tophat
curprev 08:4708:47, 27 May 2015‎ Brb talk contribs‎ 73,079 bytes +37‎ →‎FAQs for Tophat
curprev 08:4608:46, 27 May 2015‎ Brb talk contribs‎ 73,042 bytes +1,096‎ →‎Output from console

curprev 15:5415:54, 26 May 2015‎ Brb talk contribs‎ 71,946 bytes +13‎ →‎Align the reads to the reference genome using tophat2 (fastq -> bam, bed)

curprev 15:1015:10, 20 May 2015‎ Brb talk contribs‎ 64,938 bytes +38‎ →‎GEO
curprev 15:0115:01, 20 May 2015‎ Brb talk contribs‎ 64,900 bytes +79‎ →‎Other RNA-Seq data
curprev 11:1911:19, 20 May 2015‎ Brb talk contribs‎ 64,821 bytes +183‎ →‎GEO

curprev 10:5010:50, 8 May 2015‎ Brb talk contribs‎ 64,638 bytes +988‎ →‎Genomes

curprev 12:0012:00, 29 April 2015‎ Brb talk contribs‎ 47,683 bytes +141‎ →‎Organize, sort and index the BAM files and create SAM files (bam -> sam)
curprev 11:5411:54, 29 April 2015‎ Brb talk contribs‎ 47,542 bytes +192‎ →‎Organize, sort and index the BAM files and create SAM files (bam -> sam)
curprev 11:5011:50, 29 April 2015‎ Brb talk contribs‎ 47,350 bytes +12‎ →‎Organize, sort and index the BAM files and create SAM files (bam -> sam)

curprev 10:5810:58, 5 March 2015‎ Brb talk contribs‎ 47,338 bytes +100‎ →‎Human BodyMap 2.0 data from Illumina

curprev 10:0410:04, 28 January 2015‎ Brb talk contribs‎ 47,238 bytes +107‎ →‎Other RNA-Seq data

curprev 21:2421:24, 23 January 2015‎ Brb talk contribs‎ 47,131 bytes +309‎ →‎Other RNA-Seq data

curprev 15:2215:22, 20 November 2014‎ Brb talk contribs‎ 46,822 bytes +138‎ →‎Inspect alignments with IGV

curprev 14:1414:14, 15 October 2014‎ Brb talk contribs‎ 46,684 bytes +6,448‎ →‎GSE51403

curprev 18:0718:07, 11 October 2014‎ Brb talk contribs‎ 40,236 bytes +2‎ →‎Structure of downloaded reference genome from Tophat
curprev 18:0618:06, 11 October 2014‎ Brb talk contribs‎ 40,234 bytes +31‎ →‎Structure of downloaded reference genome from Tophat
curprev 17:5317:53, 11 October 2014‎ Brb talk contribs‎ 40,203 bytes +23‎ →‎Structure of downloaded reference genome from Tophat
curprev 17:4917:49, 11 October 2014‎ Brb talk contribs‎ 40,180 bytes +2,061‎ →‎Structure of downloaded reference genome from Tophat

curprev 10:1810:18, 26 September 2014‎ Brb talk contribs‎ 38,119 bytes +58‎ →‎Other RNA-Seq data

curprev 08:4308:43, 15 September 2014‎ Brb talk contribs‎ 38,061 bytes +114‎ →‎Required tools

curprev 11:1411:14, 12 August 2014‎ Brb talk contribs‎ 37,947 bytes +67‎ →‎SRA000299
curprev 09:4909:49, 12 August 2014‎ Brb talk contribs‎ 37,880 bytes +306‎ →‎SRA000299
curprev 09:3409:34, 12 August 2014‎ Brb talk contribs‎ 37,574 bytes +699‎ →‎Other RNA-Seq data

curprev 09:3109:31, 11 August 2014‎ Brb talk contribs‎ 36,875 bytes +247‎ →‎Required tools

curprev 13:4413:44, 8 August 2014‎ Brb talk contribs‎ 36,628 bytes +183‎ →‎Inspect alignments with IGV
curprev 12:3712:37, 8 August 2014‎ Brb talk contribs‎ 36,445 bytes +444‎ →‎Check Coverage from bam file
curprev 10:2610:26, 8 August 2014‎ Brb talk contribs‎ 36,001 bytes +53‎ →‎Inspect alignments with IGV

curprev 15:1215:12, 2 July 2014‎ Brb talk contribs‎ 35,948 bytes +155‎ No edit summary
curprev 14:4514:45, 2 July 2014‎ Brb talk contribs‎ 35,793 bytes +199‎ →‎Inspect alignments with IGV

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

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

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)

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)

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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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..."

Anders2013: Revision history

24 February 2016

23 February 2016

15 January 2016

31 December 2015

7 December 2015

10 November 2015

28 October 2015

19 September 2015

16 September 2015

14 September 2015

21 August 2015

19 August 2015

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17 August 2015

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7 August 2015

4 August 2015

30 July 2015

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18 July 2015

1 July 2015

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5 March 2015

28 January 2015

23 January 2015

20 November 2014

15 October 2014

11 October 2014

26 September 2014

15 September 2014

12 August 2014

11 August 2014

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2 July 2014

1 July 2014

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23 June 2014

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4 June 2014

3 June 2014

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15 May 2014

9 May 2014

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1 April 2014

31 March 2014

30 March 2014

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27 March 2014

25 March 2014

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18 March 2014

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8 March 2014

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