User contributions for Curtish@uab.edu
Jump to navigation
Jump to search
31 October 2012
- 16:4816:48, 31 October 2012 diff hist +195 NgsCcts →in process
30 October 2012
- 21:5321:53, 30 October 2012 diff hist +34 NgsCcts →Short Read (denovo) Assemblers
- 21:4921:49, 30 October 2012 diff hist +244 NgsCcts →Short Read (denovo) Assemblers
25 October 2012
- 18:2218:22, 25 October 2012 diff hist −1 PublicDatasetsNgs →Directory Structure
- 18:2118:21, 25 October 2012 diff hist −1 PublicDatasetsNgs →Public Genomes and indexes for NGS
- 18:2018:20, 25 October 2012 diff hist −1 PublicDatasetsNgs →Notes on what CCTS BMI wants to populate
- 18:1918:19, 25 October 2012 diff hist +544 PublicDatasetsNgs →Notes on what CCTS BMI wants to populate
9 October 2012
- 22:0922:09, 9 October 2012 diff hist −23 NgsCctsBuildBwa →Building BWA for /share/apps/ngs-ccts current
- 22:0822:08, 9 October 2012 diff hist +2 NgsCcts →Short Read Aligners
- 22:0722:07, 9 October 2012 diff hist +69 NgsCcts →Short Read (denovo) Assemblers
- 22:0522:05, 9 October 2012 diff hist +6 NgsCctsBuildAbyss No edit summary
- 22:0422:04, 9 October 2012 diff hist +119 NgsCctsBuildAbyss No edit summary
- 22:0322:03, 9 October 2012 diff hist +13 NgsCctsBuildAbyss No edit summary
- 21:5821:58, 9 October 2012 diff hist +58 NgsCctsBuildAbyss No edit summary
- 21:5721:57, 9 October 2012 diff hist +96 NgsCctsBuildAbyss No edit summary
- 21:5221:52, 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..."
- 21:1821:18, 9 October 2012 diff hist +229 NgsCcts →Short Read (denovo) Assemblers
- 21:1621:16, 9 October 2012 diff hist −5 NgsCcts →Short Read Aligners
- 21:1521:15, 9 October 2012 diff hist −3 NgsCcts →Short Read Aligners
- 21:1521:15, 9 October 2012 diff hist −6 NgsCcts →Short Read (denovo) Assemblers
- 21:1521:15, 9 October 2012 diff hist +111 NgsCcts →Short Read (denovo) Assemblers
- 21:0321:03, 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 ${TARGET_VER} Edit Makefile to c..."
- 20:5220:52, 9 October 2012 diff hist +29 N NgsCctsBuildBwa build Curtish@uab.edu moved page NgsCctsBuildBwa build to NgsCctsBuildBwa current
- 20:5220:52, 9 October 2012 diff hist 0 m NgsCctsBuildBwa Curtish@uab.edu moved page NgsCctsBuildBwa build to NgsCctsBuildBwa
- 20:4720:47, 9 October 2012 diff hist +393 N NgsCctsBuildBwa Created page with "= Building BWA for /share/apps/ngs-ccts = Downloading and building BWA BWA_VER=bwa-0.6.2 wget http://downloads.sourceforge.net/project/bio-bwa/${BWA_VER}.tar.bz2?r=http%3A..."
- 20:4120:41, 9 October 2012 diff hist +2 NgsCcts →Short Read Aligners
- 20:4020:40, 9 October 2012 diff hist +221 NgsCcts →Short Read Aligners
- 20:3520:35, 9 October 2012 diff hist +6 NgsCcts →Short Read Aligners
- 20:3420:34, 9 October 2012 diff hist +20 NgsCcts →Alignment Visualization
- 20:3320:33, 9 October 2012 diff hist +554 NgsCcts No edit summary
4 October 2012
- 21:0621:06, 4 October 2012 diff hist +120 PublicDatasetsNgs →Notes on what CCTS BMI wants to populate
- 17:3217:32, 4 October 2012 diff hist +210 PublicDatasetsNgs →Public Genomes and indexes for NGS
- 17:2917:29, 4 October 2012 diff hist +60 NgsCcts →Shared CCTS NGS apps
3 October 2012
- 15:3515:35, 3 October 2012 diff hist +179 PublicDatasetsNgs →Notes on what CCTS BMI wants to populate
2 October 2012
- 18:5818:58, 2 October 2012 diff hist +412 PublicDatasetsNgs →Notes on what CCTS BMI wants to populate
- 18:4918:49, 2 October 2012 diff hist +283 PublicDatasetsNgs →Notes on what CCTS BMI wants to populate
- 18:2118:21, 2 October 2012 diff hist +32 PublicDatasetsNgs →Directory Structure
- 18:2018:20, 2 October 2012 diff hist +31 N NgsGenomes Curtish@uab.edu moved page NgsGenomes to PublicDatasetsNgs: creating a sub-page of PublicDatasets current
- 18:2018:20, 2 October 2012 diff hist 0 m PublicDatasetsNgs Curtish@uab.edu moved page NgsGenomes to PublicDatasetsNgs: creating a sub-page of PublicDatasets
1 October 2012
- 18:1318:13, 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..."
12 September 2012
- 04:2904:29, 12 September 2012 diff hist +52 IgvFromComputeNode →Remote display from compute node
- 04:2304:23, 12 September 2012 diff hist +176 IgvFromComputeNode →Remote display from compute node
- 04:1004:10, 12 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]] ..."
- 03:3903:39, 12 September 2012 diff hist +343 NgsCcts →Shared CCTS NGS apps
7 September 2012
- 15:5215:52, 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"
29 February 2012
- 21:0821:08, 29 February 2012 diff hist +212 Cheaha Add physical node grid to Hardware section
13 February 2012
26 January 2012
- 18:2518:25, 26 January 2012 diff hist +59 Galaxy →FASTA File
- 18:2318:23, 26 January 2012 diff hist +87 Galaxy →Introduction
19 December 2011
- 22:2722:27, 19 December 2011 diff hist +538 GalaxyFilterCommonSnps No edit summary current
- 22:0422:04, 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:..."
13 December 2011
- 21:5621:56, 13 December 2011 diff hist +43 Galaxy →Configuration File Update
- 20:5620:56, 13 December 2011 diff hist +79 Galaxy →Index Creation
30 November 2011
- 22:1122:11, 30 November 2011 diff hist −959 Galaxy →Configuration File Update
- 22:0722:07, 30 November 2011 diff hist +5 Galaxy →Index Creation
- 22:0722:07, 30 November 2011 diff hist −1,733 Galaxy →Index Creation
4 November 2011
- 20:5620:56, 4 November 2011 diff hist +105 GalaxyAddTool →pre-requisits current
- 20:2620:26, 4 November 2011 diff hist +45 GalaxyAddTool →Creating a command-wrapper by hand
- 20:1420:14, 4 November 2011 diff hist +34 GalaxyAddTool →Creating a command-wrapper by hand
- 20:1220:12, 4 November 2011 diff hist +76 GalaxyAddTool →Creating a command-wrapper by hand
- 20:1120:11, 4 November 2011 diff hist +466 GalaxyAddTool →Creating a command-wrapper by hand
- 19:5119:51, 4 November 2011 diff hist +221 GalaxyAddTool →Creating a command-wrapper by hand
2 November 2011
- 20:5420:54, 2 November 2011 diff hist +77 GalaxyAddTool No edit summary
- 20:5120:51, 2 November 2011 diff hist +9 GalaxyAddTool →pre-requisits
- 20:5020:50, 2 November 2011 diff hist +683 GalaxyAddTool No edit summary
- 20:2420:24, 2 November 2011 diff hist +507 N GalaxyAddTool start
1 November 2011
- 17:5317:53, 1 November 2011 diff hist +6 Intermine →Web Resources
- 17:5317:53, 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..."
16 September 2011
- 14:5514:55, 16 September 2011 diff hist +501 UAB Galaxy RNA Seq Step by Step Tutorial →Track and Assemble Transcripts with CuffCompare current
- 10:1610:16, 16 September 2011 diff hist 0 N File:Transcript control vs drugged with fold.pdf.png No edit summary current
- 10:0910:09, 16 September 2011 diff hist 0 N File:Transcript control vs drugged with fold.pdf No edit summary current
- 09:3809:38, 16 September 2011 diff hist +5 UAB Galaxy RNA Seq Step by Step Tutorial →extracting the data you want
- 09:3709:37, 16 September 2011 diff hist +4,335 UAB Galaxy RNA Seq Step by Step Tutorial →Fold Change Between Conditions: CuffDiff
- 08:3708:37, 16 September 2011 diff hist −5 UAB Galaxy RNA Seq Step by Step Tutorial →cuffcompare inputs
- 08:3608:36, 16 September 2011 diff hist +85 UAB Galaxy RNA Seq Step by Step Tutorial →cuffcompare inputs
- 08:3408:34, 16 September 2011 diff hist +550 UAB Galaxy RNA Seq Step by Step Tutorial →Track and Assemble Transcripts with CuffCompare
- 08:2808:28, 16 September 2011 diff hist −2 UAB Galaxy RNA Seq Step by Step Tutorial →Track and Assemble Transcripts with CuffCompare =
- 08:2508:25, 16 September 2011 diff hist +331 Welcome add Galaxy box
- 08:2008:20, 16 September 2011 diff hist +148 Projects →Collaboration
- 08:1808:18, 16 September 2011 diff hist +203 Galaxy DNA-Seq Tutorial →Galaxy DNA-Seq Tutorial
- 08:1508:15, 16 September 2011 diff hist +1 UAB Galaxy Workshop Tutorial →Getting Started Tutorial current
- 08:1508:15, 16 September 2011 diff hist +1 UAB Galaxy Workshop Tutorial →Galaxy DNA-Seq Tutorial
- 08:1108:11, 16 September 2011 diff hist +5 UAB Galaxy Workshop Tutorial →Getting Started Tutorial
- 08:1108:11, 16 September 2011 diff hist +5 UAB Galaxy Workshop Tutorial →Galaxy DNA-Seq Tutorial
- 08:1008:10, 16 September 2011 diff hist +2 UAB Galaxy Workshop Tutorial →Galaxy DNA-Seq Tutorial
- 08:1008:10, 16 September 2011 diff hist +180 UAB Galaxy Workshop Tutorial →Galaxy DNA-Seq Tutorial
- 08:0808:08, 16 September 2011 diff hist 0 N File:RCD2011 DNA-Seq Workshop Talk.pdf No edit summary current
- 07:5907:59, 16 September 2011 diff hist +753 UAB Galaxy RNA Seq Step by Step Tutorial →Compare transcript levels: cuffdiff/cuffcompare
- 07:5007:50, 16 September 2011 diff hist +870 UAB Galaxy RNA Seq Step by Step Tutorial →Cufflinks outputs
- 07:4207:42, 16 September 2011 diff hist +32 UAB Galaxy RNA Seq Step by Step Tutorial →Cufflinks inputs
- 07:4007:40, 16 September 2011 diff hist +1 UAB Galaxy RNA Seq Step by Step Tutorial →Cufflinks inputs
- 07:3907:39, 16 September 2011 diff hist +1,083 UAB Galaxy RNA Seq Step by Step Tutorial →Construct transcripts using Cufflinks
- 07:2407:24, 16 September 2011 diff hist +457 UAB Galaxy RNA Seq Step by Step Tutorial →Alignment/Mapping QC
- 07:1307:13, 16 September 2011 diff hist +94 UAB Galaxy RNA Seq Step by Step Tutorial →Alignment/Mapping QC
- 07:1307:13, 16 September 2011 diff hist 0 N File:Tophat accepted hits BAM IGV Sox6.png No edit summary current
- 06:5306:53, 16 September 2011 diff hist +31 Galaxy →Using Galaxy / Tutorials
- 06:5206:52, 16 September 2011 diff hist +2 UAB Galaxy RNA Seq Step by Step Tutorial →Alignment/Mapping QC
- 06:5106:51, 16 September 2011 diff hist +35 UAB Galaxy RNA Seq Step by Step Tutorial →Alignment/Mapping QC
- 06:4506:45, 16 September 2011 diff hist +7 UAB Galaxy RNA Seq Step by Step Tutorial →Alignment/Mapping QC
- 06:4506:45, 16 September 2011 diff hist +8 UAB Galaxy RNA Seq Step by Step Tutorial →TopHat output