User contributions
(Latest | Earliest) View (newer 500 | older 500) (20 | 50 | 100 | 250 | 500)
- 15:58, 9 October 2012 (diff | hist) . . (+58) . . NgsCctsBuildAbyss
- 15:57, 9 October 2012 (diff | hist) . . (+96) . . NgsCctsBuildAbyss
- 15:52, 9 October 2012 (diff | hist) . . (+928) . . N NgsCctsBuildAbyss (Created page with " Based on [file:///share/apps/ngs-ccts/abyss-1.3.4/README.html#compilingabyssfromsource README.html:compiling from source] Requires [sparsehash] TARGET_VER=sparsehash-2.0.2...")
- 15:18, 9 October 2012 (diff | hist) . . (+229) . . NgsCcts (→Short Read (denovo) Assemblers)
- 15:16, 9 October 2012 (diff | hist) . . (-5) . . NgsCcts (→Short Read Aligners)
- 15:15, 9 October 2012 (diff | hist) . . (-3) . . NgsCcts (→Short Read Aligners)
- 15:15, 9 October 2012 (diff | hist) . . (-6) . . NgsCcts (→Short Read (denovo) Assemblers)
- 15:15, 9 October 2012 (diff | hist) . . (+111) . . NgsCcts (→Short Read (denovo) Assemblers)
- 15:03, 9 October 2012 (diff | hist) . . (+277) . . N NgsCctsBuildVelvet (Created page with " TARGET_VER=velvet_1.2.08 wget http://www.ebi.ac.uk/~zerbino/velvet/${TARGET_VER}.tgz tar xzvf ${TARGET_VER}.tgz rm ${TARGET_VER}.tgz cd ${TARGET_VER} Edit Makefile to c...")
- 14:52, 9 October 2012 (diff | hist) . . (+29) . . N NgsCctsBuildBwa build (Curtish@uab.edu moved page NgsCctsBuildBwa build to NgsCctsBuildBwa) (top)
- 14:52, 9 October 2012 (diff | hist) . . (0) . . m NgsCctsBuildBwa (Curtish@uab.edu moved page NgsCctsBuildBwa build to NgsCctsBuildBwa)
- 14:47, 9 October 2012 (diff | hist) . . (+393) . . N NgsCctsBuildBwa (Created page with "= Building BWA for /share/apps/ngs-ccts = Downloading and building BWA BWA_VER=bwa-0.6.2 wget http://downloads.sourceforge.net/project/bio-bwa/${BWA_VER}.tar.bz2?r=http%3A...")
- 14:41, 9 October 2012 (diff | hist) . . (+2) . . NgsCcts (→Short Read Aligners)
- 14:40, 9 October 2012 (diff | hist) . . (+221) . . NgsCcts (→Short Read Aligners)
- 14:35, 9 October 2012 (diff | hist) . . (+6) . . NgsCcts (→Short Read Aligners)
- 14:34, 9 October 2012 (diff | hist) . . (+20) . . NgsCcts (→Alignment Visualization)
- 14:33, 9 October 2012 (diff | hist) . . (+554) . . NgsCcts
- 15:06, 4 October 2012 (diff | hist) . . (+120) . . PublicDatasetsNgs (→Notes on what CCTS BMI wants to populate)
- 11:32, 4 October 2012 (diff | hist) . . (+210) . . PublicDatasetsNgs (→Public Genomes and indexes for NGS)
- 11:29, 4 October 2012 (diff | hist) . . (+60) . . NgsCcts (→Shared CCTS NGS apps)
- 09:35, 3 October 2012 (diff | hist) . . (+179) . . PublicDatasetsNgs (→Notes on what CCTS BMI wants to populate)
- 12:58, 2 October 2012 (diff | hist) . . (+412) . . PublicDatasetsNgs (→Notes on what CCTS BMI wants to populate)
- 12:49, 2 October 2012 (diff | hist) . . (+283) . . PublicDatasetsNgs (→Notes on what CCTS BMI wants to populate)
- 12:21, 2 October 2012 (diff | hist) . . (+32) . . PublicDatasetsNgs (→Directory Structure)
- 12:20, 2 October 2012 (diff | hist) . . (+31) . . N NgsGenomes (Curtish@uab.edu moved page NgsGenomes to PublicDatasetsNgs: creating a sub-page of PublicDatasets) (top)
- 12:20, 2 October 2012 (diff | hist) . . (0) . . m PublicDatasetsNgs (Curtish@uab.edu moved page NgsGenomes to PublicDatasetsNgs: creating a sub-page of PublicDatasets)
- 12:13, 1 October 2012 (diff | hist) . . (+2,402) . . N PublicDatasetsNgs (Created page with "= Public Genomes and indexes for NGS = CCTS BMI in conjunection with anyone who wishes to participate, maintains a public directory of genomic sequences and indexes built fro...")
- 22:29, 11 September 2012 (diff | hist) . . (+52) . . IgvFromComputeNode (→Remote display from compute node)
- 22:23, 11 September 2012 (diff | hist) . . (+176) . . IgvFromComputeNode (→Remote display from compute node)
- 22:10, 11 September 2012 (diff | hist) . . (+654) . . N IgvFromComputeNode (Created page with "= Remote display from compute node = Example program: IGV # Install & Launch X-Win on your desktop machine * Windows: X-Win32 from [http://www.uab.edu/it/software UAB IT]] ...")
- 21:39, 11 September 2012 (diff | hist) . . (+343) . . NgsCcts (→Shared CCTS NGS apps)
- 09:52, 7 September 2012 (diff | hist) . . (+113) . . N NgsCcts (Created page with "= Shared CCTS NGS apps = This page documents apps installed by the CCTS BMI group in cheaha:/share/apps/ngs-ccts")
- 15:08, 29 February 2012 (diff | hist) . . (+212) . . Cheaha (Add physical node grid to Hardware section)
- 09:38, 13 February 2012 (diff | hist) . . (+7) . . m SubversionOverHttps (→Download user certificate)
- 12:25, 26 January 2012 (diff | hist) . . (+59) . . Galaxy (→FASTA File)
- 12:23, 26 January 2012 (diff | hist) . . (+87) . . Galaxy (→Introduction)
- 16:27, 19 December 2011 (diff | hist) . . (+538) . . GalaxyFilterCommonSnps (top)
- 16:04, 19 December 2011 (diff | hist) . . (+2,269) . . N GalaxyFilterCommonSnps (Created page with "Protocol for Filtering common SNPs from a set of alignments Galaxy supports set operations on single columns. Thus, I build an index column for each sample formated as "chr:pos:...")
- 15:56, 13 December 2011 (diff | hist) . . (+43) . . Galaxy (→Configuration File Update)
- 14:56, 13 December 2011 (diff | hist) . . (+79) . . Galaxy (→Index Creation)
- 16:11, 30 November 2011 (diff | hist) . . (-959) . . Galaxy (→Configuration File Update)
- 16:07, 30 November 2011 (diff | hist) . . (+5) . . Galaxy (→Index Creation)
- 16:07, 30 November 2011 (diff | hist) . . (-1,733) . . Galaxy (→Index Creation)
- 14:56, 4 November 2011 (diff | hist) . . (+105) . . GalaxyAddTool (→pre-requisits) (top)
- 14:26, 4 November 2011 (diff | hist) . . (+45) . . GalaxyAddTool (→Creating a command-wrapper by hand)
- 14:14, 4 November 2011 (diff | hist) . . (+34) . . GalaxyAddTool (→Creating a command-wrapper by hand)
- 14:12, 4 November 2011 (diff | hist) . . (+76) . . GalaxyAddTool (→Creating a command-wrapper by hand)
- 14:11, 4 November 2011 (diff | hist) . . (+466) . . GalaxyAddTool (→Creating a command-wrapper by hand)
- 13:51, 4 November 2011 (diff | hist) . . (+221) . . GalaxyAddTool (→Creating a command-wrapper by hand)
- 14:54, 2 November 2011 (diff | hist) . . (+77) . . GalaxyAddTool
- 14:51, 2 November 2011 (diff | hist) . . (+9) . . GalaxyAddTool (→pre-requisits)
- 14:50, 2 November 2011 (diff | hist) . . (+683) . . GalaxyAddTool
- 14:24, 2 November 2011 (diff | hist) . . (+507) . . N GalaxyAddTool (start)
- 11:53, 1 November 2011 (diff | hist) . . (+6) . . Intermine (→Web Resources)
- 11:53, 1 November 2011 (diff | hist) . . (+560) . . N Intermine (Created page with "== Motivation == CCTS/BMI group plans to establish an Intermine server at UAB in order to support genomics (and other -omic) reseach. The tool provides a way to link datasets w...")
- 08:55, 16 September 2011 (diff | hist) . . (+501) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Track and Assemble Transcripts with CuffCompare) (top)
- 04:16, 16 September 2011 (diff | hist) . . (0) . . N File:Transcript control vs drugged with fold.pdf.png (top)
- 04:09, 16 September 2011 (diff | hist) . . (0) . . N File:Transcript control vs drugged with fold.pdf (top)
- 03:38, 16 September 2011 (diff | hist) . . (+5) . . UAB Galaxy RNA Seq Step by Step Tutorial (→extracting the data you want)
- 03:37, 16 September 2011 (diff | hist) . . (+4,335) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Fold Change Between Conditions: CuffDiff)
- 02:37, 16 September 2011 (diff | hist) . . (-5) . . UAB Galaxy RNA Seq Step by Step Tutorial (→cuffcompare inputs)
- 02:36, 16 September 2011 (diff | hist) . . (+85) . . UAB Galaxy RNA Seq Step by Step Tutorial (→cuffcompare inputs)
- 02:34, 16 September 2011 (diff | hist) . . (+550) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Track and Assemble Transcripts with CuffCompare)
- 02:28, 16 September 2011 (diff | hist) . . (-2) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Track and Assemble Transcripts with CuffCompare =)
- 02:25, 16 September 2011 (diff | hist) . . (+331) . . Welcome (add Galaxy box)
- 02:20, 16 September 2011 (diff | hist) . . (+148) . . Projects (→Collaboration)
- 02:18, 16 September 2011 (diff | hist) . . (+203) . . Galaxy DNA-Seq Tutorial (→Galaxy DNA-Seq Tutorial)
- 02:15, 16 September 2011 (diff | hist) . . (+1) . . UAB Galaxy Workshop Tutorial (→Getting Started Tutorial) (top)
- 02:15, 16 September 2011 (diff | hist) . . (+1) . . UAB Galaxy Workshop Tutorial (→Galaxy DNA-Seq Tutorial)
- 02:11, 16 September 2011 (diff | hist) . . (+5) . . UAB Galaxy Workshop Tutorial (→Getting Started Tutorial)
- 02:11, 16 September 2011 (diff | hist) . . (+5) . . UAB Galaxy Workshop Tutorial (→Galaxy DNA-Seq Tutorial)
- 02:10, 16 September 2011 (diff | hist) . . (+2) . . UAB Galaxy Workshop Tutorial (→Galaxy DNA-Seq Tutorial)
- 02:10, 16 September 2011 (diff | hist) . . (+180) . . UAB Galaxy Workshop Tutorial (→Galaxy DNA-Seq Tutorial)
- 02:08, 16 September 2011 (diff | hist) . . (0) . . N File:RCD2011 DNA-Seq Workshop Talk.pdf (top)
- 01:59, 16 September 2011 (diff | hist) . . (+753) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Compare transcript levels: cuffdiff/cuffcompare)
- 01:50, 16 September 2011 (diff | hist) . . (+870) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Cufflinks outputs)
- 01:42, 16 September 2011 (diff | hist) . . (+32) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Cufflinks inputs)
- 01:40, 16 September 2011 (diff | hist) . . (+1) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Cufflinks inputs)
- 01:39, 16 September 2011 (diff | hist) . . (+1,083) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Construct transcripts using Cufflinks)
- 01:24, 16 September 2011 (diff | hist) . . (+457) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Alignment/Mapping QC)
- 01:13, 16 September 2011 (diff | hist) . . (+94) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Alignment/Mapping QC)
- 01:13, 16 September 2011 (diff | hist) . . (0) . . N File:Tophat accepted hits BAM IGV Sox6.png (top)
- 00:53, 16 September 2011 (diff | hist) . . (+31) . . Galaxy (→Using Galaxy / Tutorials)
- 00:52, 16 September 2011 (diff | hist) . . (+2) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Alignment/Mapping QC)
- 00:51, 16 September 2011 (diff | hist) . . (+35) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Alignment/Mapping QC)
- 00:45, 16 September 2011 (diff | hist) . . (+7) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Alignment/Mapping QC)
- 00:45, 16 September 2011 (diff | hist) . . (+8) . . UAB Galaxy RNA Seq Step by Step Tutorial (→TopHat output)
- 00:42, 16 September 2011 (diff | hist) . . (-8) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Align using TopHat: inputs)
- 00:41, 16 September 2011 (diff | hist) . . (-2) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Tophat Inputs)
- 00:41, 16 September 2011 (diff | hist) . . (+22) . . UAB Galaxy RNA Seq Step by Step Tutorial (→NGS: RNA Analysis > Tophat for Illumina)
- 00:39, 16 September 2011 (diff | hist) . . (-18) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Align using TopHat: inputs)
- 00:39, 16 September 2011 (diff | hist) . . (+34) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Check quality of READ data)
- 00:38, 16 September 2011 (diff | hist) . . (+133) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Check quality of READ data)
- 00:34, 16 September 2011 (diff | hist) . . (-1) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Upload data)
- 00:33, 16 September 2011 (diff | hist) . . (+41) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Upload data)
- 00:31, 16 September 2011 (diff | hist) . . (+37) . . UAB Galaxy Workshop Tutorial (→Galaxy DNA-Seq Tutorial)
- 00:31, 16 September 2011 (diff | hist) . . (+77) . . UAB Galaxy Workshop Tutorial (→Galaxy RNA-Seq Tutorial)
- 00:30, 16 September 2011 (diff | hist) . . (+264) . . UAB Galaxy Workshop Tutorial (→Galaxy RNA-Seq Tutorial)
- 00:26, 16 September 2011 (diff | hist) . . (-38) . . UAB Galaxy Workshop Tutorial (→UAB Galaxy Tutorial)
- 00:24, 16 September 2011 (diff | hist) . . (-127) . . UAB Galaxy Workshop Tutorial (→Galaxy Data Import)
- 00:15, 16 September 2011 (diff | hist) . . (+164) . . 2011 HPC Boot Camp (→Agenda)
- 00:10, 16 September 2011 (diff | hist) . . (+37) . . Galaxy
- 21:20, 15 September 2011 (diff | hist) . . (+150) . . UAB Galaxy RNA Seq Step by Step Tutorial (→File Types and Acronyms)
- 15:21, 15 September 2011 (diff | hist) . . (+243) . . UAB Galaxy Workshop Tutorial (→Overview)
- 15:16, 15 September 2011 (diff | hist) . . (0) . . File:RCD 2011 Welcome to Galaxy tutorial.pdf (uploaded a new version of "File:RCD 2011 Welcome to Galaxy tutorial.pdf": Original PPT (with animatoins) at ftp://ftp.genome.uab.edu/ICS/Galaxy_RNAseq_tutorial/RCD%202011%20Welcome%20to%20Galaxy%20tutorial.pptx) (top)
- 15:12, 15 September 2011 (diff | hist) . . (0) . . N File:RCD 2011 Welcome to Galaxy tutorial.pdf
- 13:52, 14 September 2011 (diff | hist) . . (+27) . . UAB Galaxy RNA Seq Step by Step Tutorial (→File Types)
- 13:51, 14 September 2011 (diff | hist) . . (+497) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Construct transcripts : Cufflinks)
- 13:43, 14 September 2011 (diff | hist) . . (-5) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Menu: [NGS: RNA Analysis > Tophat for Illumina ])
- 13:41, 14 September 2011 (diff | hist) . . (+9) . . UAB Galaxy RNA Seq Step by Step Tutorial (→QC alignment)
- 13:39, 14 September 2011 (diff | hist) . . (+6) . . UAB Galaxy RNA Seq Step by Step Tutorial (→QC alignment)
- 13:39, 14 September 2011 (diff | hist) . . (+39) . . UAB Galaxy RNA Seq Step by Step Tutorial (→QC alignment)
- 13:38, 14 September 2011 (diff | hist) . . (+81) . . UAB Galaxy RNA Seq Step by Step Tutorial (→QC alignment)
- 13:37, 14 September 2011 (diff | hist) . . (+1,560) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Align using TopHat: inputs)
- 13:20, 14 September 2011 (diff | hist) . . (+106) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Check quality of READ data)
- 13:18, 14 September 2011 (diff | hist) . . (+4) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Upload data)
- 13:18, 14 September 2011 (diff | hist) . . (+404) . . UAB Galaxy RNA Seq Step by Step Tutorial
- 09:42, 14 September 2011 (diff | hist) . . (+80) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Check quality of data)
- 09:41, 14 September 2011 (diff | hist) . . (+46) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Web Resources)
- 09:40, 14 September 2011 (diff | hist) . . (+91) . . UAB Galaxy RNA Seq Step by Step Tutorial (→File Types)
- 09:39, 14 September 2011 (diff | hist) . . (+316) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Web Resources)
- 21:12, 13 September 2011 (diff | hist) . . (+753) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Upload data)
- 20:52, 13 September 2011 (diff | hist) . . (+31) . . UAB Galaxy RNA Seq Step by Step Tutorial (→File Types)
- 20:49, 13 September 2011 (diff | hist) . . (+1,056) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Galaxy RNA-Seq Step-by-Step Tutorial/Protocol)
- 15:52, 13 September 2011 (diff | hist) . . (+429) . . UAB Galaxy RNA Seq Step by Step Tutorial (→TopHat output)
- 15:40, 13 September 2011 (diff | hist) . . (+134) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Menu: [NGS: RNA Analysis > Tophat for Illumina ])
- 15:32, 13 September 2011 (diff | hist) . . (+62) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Align using TopHat)
- 15:29, 13 September 2011 (diff | hist) . . (+56) . . N File:Ha gsl insert group.png (Example insert fragment length file from HudsonAlpha GSL) (top)
- 15:28, 13 September 2011 (diff | hist) . . (+410) . . UAB Galaxy RNA Seq Step by Step Tutorial
- 14:48, 13 September 2011 (diff | hist) . . (+625) . . UAB Galaxy RNA Seq Step by Step Tutorial
- 14:33, 13 September 2011 (diff | hist) . . (+1,215) . . UAB Galaxy RNA Seq Step by Step Tutorial
- 13:40, 13 September 2011 (diff | hist) . . (+538) . . UAB Galaxy RNA Seq Step by Step Tutorial (→Upload data)
- 12:59, 13 September 2011 (diff | hist) . . (-5) . . UAB Galaxy Workshop Tutorial (→Getting data into Galaxy)
- 12:57, 13 September 2011 (diff | hist) . . (+43) . . UAB Galaxy Workshop Tutorial (→Getting data into Galaxy)
- 12:57, 13 September 2011 (diff | hist) . . (+392) . . N UAB Galaxy RNA Seq Step by Step Tutorial (outline)
- 10:29, 8 September 2011 (diff | hist) . . (+36) . . 2011 HPC Boot Camp (→Agenda)
- 10:27, 8 September 2011 (diff | hist) . . (+49) . . 2011 HPC Boot Camp (→Agenda)
- 10:24, 8 September 2011 (diff | hist) . . (+135) . . 2011 HPC Boot Camp (→Agenda)
- 11:10, 18 August 2011 (diff | hist) . . (-22) . . GalaxyNgs (top)
- 11:09, 18 August 2011 (diff | hist) . . (+2,571) . . N GalaxyNgs (Quick Notes on NGS sequencing analysis using our Galaxy app)
- 09:56, 27 July 2011 (diff | hist) . . (+92) . . UploadLargeData
- 14:01, 8 July 2011 (diff | hist) . . (+174) . . UploadLargeData (→transfer and uncompress (slow))
- 14:56, 23 June 2011 (diff | hist) . . (+297) . . UploadLargeData
- 16:02, 22 June 2011 (diff | hist) . . (+177) . . UploadLargeData
- 14:49, 22 June 2011 (diff | hist) . . (+1,431) . . N UploadLargeData (Created page with "= Load and Link approach = == transfer and uncompress (slow) == # login to cheaha.uabgrid.uab.edu (linux), # create directory for this data set in your scratch dir ## mkdir /l...")
- 14:09, 22 June 2011 (diff | hist) . . (-1) . . Galaxy
- 14:09, 22 June 2011 (diff | hist) . . (+170) . . Galaxy
(Latest | Earliest) View (newer 500 | older 500) (20 | 50 | 100 | 250 | 500)
