User contributions for Curtish@uab.edu
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9 October 2012
- 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
- 06:4206:42, 16 September 2011 diff hist −8 UAB Galaxy RNA Seq Step by Step Tutorial →Align using TopHat: inputs
- 06:4106:41, 16 September 2011 diff hist −2 UAB Galaxy RNA Seq Step by Step Tutorial →Tophat Inputs
- 06:4106:41, 16 September 2011 diff hist +22 UAB Galaxy RNA Seq Step by Step Tutorial →NGS: RNA Analysis > Tophat for Illumina
- 06:3906:39, 16 September 2011 diff hist −18 UAB Galaxy RNA Seq Step by Step Tutorial →Align using TopHat: inputs
- 06:3906:39, 16 September 2011 diff hist +34 UAB Galaxy RNA Seq Step by Step Tutorial →Check quality of READ data
- 06:3806:38, 16 September 2011 diff hist +133 UAB Galaxy RNA Seq Step by Step Tutorial →Check quality of READ data
- 06:3406:34, 16 September 2011 diff hist −1 UAB Galaxy RNA Seq Step by Step Tutorial →Upload data
- 06:3306:33, 16 September 2011 diff hist +41 UAB Galaxy RNA Seq Step by Step Tutorial →Upload data
- 06:3106:31, 16 September 2011 diff hist +37 UAB Galaxy Workshop Tutorial →Galaxy DNA-Seq Tutorial
- 06:3106:31, 16 September 2011 diff hist +77 UAB Galaxy Workshop Tutorial →Galaxy RNA-Seq Tutorial
- 06:3006:30, 16 September 2011 diff hist +264 UAB Galaxy Workshop Tutorial →Galaxy RNA-Seq Tutorial
- 06:2606:26, 16 September 2011 diff hist −38 UAB Galaxy Workshop Tutorial →UAB Galaxy Tutorial
- 06:2406:24, 16 September 2011 diff hist −127 UAB Galaxy Workshop Tutorial →Galaxy Data Import
- 06:1506:15, 16 September 2011 diff hist +164 2011 HPC Boot Camp →Agenda
- 06:1006:10, 16 September 2011 diff hist +37 Galaxy No edit summary
- 03:2003:20, 16 September 2011 diff hist +150 UAB Galaxy RNA Seq Step by Step Tutorial →File Types and Acronyms
15 September 2011
- 21:2121:21, 15 September 2011 diff hist +243 UAB Galaxy Workshop Tutorial →Overview
- 21:1621:16, 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 current
- 21:1221:12, 15 September 2011 diff hist 0 N File:RCD 2011 Welcome to Galaxy tutorial.pdf No edit summary
14 September 2011
- 19:5219:52, 14 September 2011 diff hist +27 UAB Galaxy RNA Seq Step by Step Tutorial →File Types
- 19:5119:51, 14 September 2011 diff hist +497 UAB Galaxy RNA Seq Step by Step Tutorial →Construct transcripts : Cufflinks
- 19:4319:43, 14 September 2011 diff hist −5 UAB Galaxy RNA Seq Step by Step Tutorial →Menu: [NGS: RNA Analysis > Tophat for Illumina ]
- 19:4119:41, 14 September 2011 diff hist +9 UAB Galaxy RNA Seq Step by Step Tutorial →QC alignment
- 19:3919:39, 14 September 2011 diff hist +6 UAB Galaxy RNA Seq Step by Step Tutorial →QC alignment
- 19:3919:39, 14 September 2011 diff hist +39 UAB Galaxy RNA Seq Step by Step Tutorial →QC alignment
- 19:3819:38, 14 September 2011 diff hist +81 UAB Galaxy RNA Seq Step by Step Tutorial →QC alignment
- 19:3719:37, 14 September 2011 diff hist +1,560 UAB Galaxy RNA Seq Step by Step Tutorial →Align using TopHat: inputs
- 19:2019:20, 14 September 2011 diff hist +106 UAB Galaxy RNA Seq Step by Step Tutorial →Check quality of READ data
- 19:1819:18, 14 September 2011 diff hist +4 UAB Galaxy RNA Seq Step by Step Tutorial →Upload data
- 19:1819:18, 14 September 2011 diff hist +404 UAB Galaxy RNA Seq Step by Step Tutorial No edit summary
- 15:4215:42, 14 September 2011 diff hist +80 UAB Galaxy RNA Seq Step by Step Tutorial →Check quality of data
- 15:4115:41, 14 September 2011 diff hist +46 UAB Galaxy RNA Seq Step by Step Tutorial →Web Resources
- 15:4015:40, 14 September 2011 diff hist +91 UAB Galaxy RNA Seq Step by Step Tutorial →File Types
- 15:3915:39, 14 September 2011 diff hist +316 UAB Galaxy RNA Seq Step by Step Tutorial →Web Resources
- 03:1203:12, 14 September 2011 diff hist +753 UAB Galaxy RNA Seq Step by Step Tutorial →Upload data
- 02:5202:52, 14 September 2011 diff hist +31 UAB Galaxy RNA Seq Step by Step Tutorial →File Types
- 02:4902:49, 14 September 2011 diff hist +1,056 UAB Galaxy RNA Seq Step by Step Tutorial →Galaxy RNA-Seq Step-by-Step Tutorial/Protocol
13 September 2011
- 21:5221:52, 13 September 2011 diff hist +429 UAB Galaxy RNA Seq Step by Step Tutorial →TopHat output
- 21:4021:40, 13 September 2011 diff hist +134 UAB Galaxy RNA Seq Step by Step Tutorial →Menu: [NGS: RNA Analysis > Tophat for Illumina ]
- 21:3221:32, 13 September 2011 diff hist +62 UAB Galaxy RNA Seq Step by Step Tutorial →Align using TopHat
- 21:2921:29, 13 September 2011 diff hist +56 N File:Ha gsl insert group.png Example insert fragment length file from HudsonAlpha GSL current
- 21:2821:28, 13 September 2011 diff hist +410 UAB Galaxy RNA Seq Step by Step Tutorial No edit summary
- 20:4820:48, 13 September 2011 diff hist +625 UAB Galaxy RNA Seq Step by Step Tutorial No edit summary
- 20:3320:33, 13 September 2011 diff hist +1,215 UAB Galaxy RNA Seq Step by Step Tutorial No edit summary
- 19:4019:40, 13 September 2011 diff hist +538 UAB Galaxy RNA Seq Step by Step Tutorial →Upload data
- 18:5918:59, 13 September 2011 diff hist −5 UAB Galaxy Workshop Tutorial →Getting data into Galaxy
- 18:5718:57, 13 September 2011 diff hist +43 UAB Galaxy Workshop Tutorial →Getting data into Galaxy
- 18:5718:57, 13 September 2011 diff hist +392 N UAB Galaxy RNA Seq Step by Step Tutorial outline
8 September 2011
- 16:2916:29, 8 September 2011 diff hist +36 2011 HPC Boot Camp →Agenda
- 16:2716:27, 8 September 2011 diff hist +49 2011 HPC Boot Camp →Agenda
- 16:2416:24, 8 September 2011 diff hist +135 2011 HPC Boot Camp →Agenda
18 August 2011
- 17:1017:10, 18 August 2011 diff hist −22 GalaxyNgs No edit summary current
- 17:0917:09, 18 August 2011 diff hist +2,571 N GalaxyNgs Quick Notes on NGS sequencing analysis using our Galaxy app
27 July 2011
- 15:5615:56, 27 July 2011 diff hist +92 UploadLargeData No edit summary
8 July 2011
23 June 2011
- 20:5620:56, 23 June 2011 diff hist +297 UploadLargeData No edit summary
22 June 2011
- 22:0222:02, 22 June 2011 diff hist +177 UploadLargeData No edit summary
- 20:4920:49, 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..."
- 20:0920:09, 22 June 2011 diff hist −1 Galaxy No edit summary
- 20:0920:09, 22 June 2011 diff hist +170 Galaxy No edit summary