User contributions for Ozborn@uab.edu
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15 September 2011
- 19:1419:14, 15 September 2011 diff hist +30 Galaxy DNA-Seq Tutorial No edit summary
- 19:1119:11, 15 September 2011 diff hist +98 Galaxy DNA-Seq Tutorial →Reference Genome
- 19:0919:09, 15 September 2011 diff hist +114 Galaxy DNA-Seq Tutorial No edit summary
- 19:0419:04, 15 September 2011 diff hist +465 Galaxy DNA-Seq Tutorial FastQC and Compute stats cleanup
- 18:4718:47, 15 September 2011 diff hist 0 N File:FastQCRunSettings.jpg No edit summary current
- 18:3918:39, 15 September 2011 diff hist +127 Galaxy DNA-Seq Tutorial No edit summary
- 18:3218:32, 15 September 2011 diff hist +115 Galaxy DNA-Seq Tutorial →Reference Genome
- 18:3018:30, 15 September 2011 diff hist +217 Galaxy →Available datasets: Added new datasets
- 18:2118:21, 15 September 2011 diff hist +368 Galaxy DNA-Seq Tutorial No edit summary
- 18:0918:09, 15 September 2011 diff hist +66 Galaxy DNA-Seq Tutorial →Linking to data
- 18:0818:08, 15 September 2011 diff hist 0 N File:DataLibraryVacWRFastQ.jpg No edit summary current
- 15:5615:56, 15 September 2011 diff hist +38 Galaxy DNA-Seq Tutorial Pileup filtering
- 15:5515:55, 15 September 2011 diff hist +35 N File:PileupFiltering100Reads.jpg Pileup run settings for Vaccinia WR current
- 05:1305:13, 15 September 2011 diff hist +75 Galaxy DNA-Seq Tutorial Filtering SNPs
- 05:1105:11, 15 September 2011 diff hist +50 N File:FilterRunVacWR.jpg How to filter a SAM file for SNPs versus reference current
- 04:2204:22, 15 September 2011 diff hist +32 Galaxy DNA-Seq Tutorial No edit summary
- 04:2104:21, 15 September 2011 diff hist +27 N File:SNPEffResults.jpg SNP Results for Vaccinia WR current
- 04:2004:20, 15 September 2011 diff hist +141 Galaxy DNA-Seq Tutorial No edit summary
- 04:1804:18, 15 September 2011 diff hist +17 N File:SNPEffCoverage.jpg For a vaccinia WR current
- 04:1704:17, 15 September 2011 diff hist +214 Galaxy DNA-Seq Tutorial SNPEff separate section
- 03:4703:47, 15 September 2011 diff hist +78 Galaxy DNA-Seq Tutorial →Variant Analysis
- 03:4503:45, 15 September 2011 diff hist +19 N File:SNPEff.jpg SNPEff run settings current
- 03:3803:38, 15 September 2011 diff hist +127 Galaxy DNA-Seq Tutorial →BAM Conversion
- 03:3403:34, 15 September 2011 diff hist +153 Galaxy DNA-Seq Tutorial →Variant Analysis
- 03:0903:09, 15 September 2011 diff hist +107 Galaxy DNA-Seq Tutorial →Variant Analysis
- 03:0803:08, 15 September 2011 diff hist +44 N File:GeneratePileup.jpg Generate pileup for Vaccinia, call consensus current
- 03:0603:06, 15 September 2011 diff hist +20 Galaxy DNA-Seq Tutorial →Looking at differences with SNPEff
14 September 2011
- 22:3622:36, 14 September 2011 diff hist +22 Galaxy DNA-Seq Tutorial Flagstat
- 22:3522:35, 14 September 2011 diff hist +29 N File:Sam2bam.jpg Conversion of SAM file to BAM current
- 22:3522:35, 14 September 2011 diff hist +44 Galaxy DNA-Seq Tutorial Flagstat
- 22:3522:35, 14 September 2011 diff hist +22 N File:Flagstat.jpg Flag stat on BAM files current
- 21:5321:53, 14 September 2011 diff hist −1 Galaxy DNA-Seq Tutorial →Short read alignment to reference genome using BWA
- 21:5221:52, 14 September 2011 diff hist +26 N File:Bwa run cmv 227r.jpg BWA run of VAC WR CMV 227R current
- 21:3321:33, 14 September 2011 diff hist +31 Galaxy DNA-Seq Tutorial →Short read alignment to reference genome using BWA
- 21:3321:33, 14 September 2011 diff hist +39 N File:Bwa run cmv 21950r.jpg Running BWA on CMV 21950R in UAB Galaxy current
- 21:0821:08, 14 September 2011 diff hist 0 File:Cmv21950r 3 1 original boxplot.jpg uploaded a new version of "File:Cmv21950r 3 1 original boxplot.jpg" current
- 21:0521:05, 14 September 2011 diff hist +38 Galaxy DNA-Seq Tutorial →Assessing the quality of the data
- 21:0421:04, 14 September 2011 diff hist 0 N File:DrawQualityScoreBoxplot.jpg No edit summary
- 20:5920:59, 14 September 2011 diff hist +44 Galaxy DNA-Seq Tutorial →Performing cleanup
- 20:5820:58, 14 September 2011 diff hist +47 N File:Cmv21950r 3 1 trimmed boxplot.jpg CMV 21950R after trimming one base off the end. current
- 20:3320:33, 14 September 2011 diff hist +43 Galaxy DNA-Seq Tutorial Adding pre-trim boxplot
- 20:3220:32, 14 September 2011 diff hist +49 N File:Cmv21950r 3 1 original boxplot.jpg Original boxplot before trimming of Vac WR 21950R
- 20:2720:27, 14 September 2011 diff hist +49 Galaxy DNA-Seq Tutorial Adding computation of qualitys stats
- 20:2520:25, 14 September 2011 diff hist +45 N File:ComputeQualityStatsCMV21950R 3 1.jpg Image of running computation of quality stats current
13 September 2011
- 22:3422:34, 13 September 2011 diff hist +212 Galaxy DNA-Seq Tutorial →Assessing the quality of the data
- 22:3122:31, 13 September 2011 diff hist +48 N File:CMV VAC WR 3 2 base quality.jpg CMV_VAC_WR_3_2 box and whiskers plot from FastQC current
- 22:3022:30, 13 September 2011 diff hist +396 Galaxy DNA-Seq Tutorial →Assessing the quality of the data
- 21:4621:46, 13 September 2011 diff hist +619 Galaxy DNA-Seq Tutorial Formatting data
- 21:3121:31, 13 September 2011 diff hist +70 N File:DataType.jpg Data attributes for a vaccinia virus fastq file from the history pane. current
- 21:2921:29, 13 September 2011 diff hist +362 Galaxy DNA-Seq Tutorial →Linking to data
- 21:2621:26, 13 September 2011 diff hist +66 N File:HistoryPane.jpg What your history pane should look like after linking in the data. current
- 19:3419:34, 13 September 2011 diff hist +437 Galaxy DNA-Seq Tutorial Linking in WR data
- 19:0519:05, 13 September 2011 diff hist +219 UAB Galaxy Workshop Tutorial No edit summary
- 19:0119:01, 13 September 2011 diff hist −48 UAB Galaxy Workshop Tutorial No edit summary
- 18:5718:57, 13 September 2011 diff hist +316 N Galaxy DNA-Seq Tutorial Created page with "= Galaxy DNA-Seq Tutorial = == Linking to data == == Grommin Data == == Assessing the quality of the data == == Performing cleanup == == Short read alignment to referenc..."
- 18:5518:55, 13 September 2011 diff hist −243 UAB Galaxy Workshop Tutorial Moving DNA-Seq and RNA-Seq to their own pages
- 17:5917:59, 13 September 2011 diff hist +123 UAB Galaxy Workshop Tutorial →Getting data into Galaxy: Added links to data uploading, still need cleanup.
- 17:5417:54, 13 September 2011 diff hist +36 UploadLargeData Added image
- 17:5117:51, 13 September 2011 diff hist +57 N File:UploadLinkDataFilesGUI.jpg Picture of linking in directory of files to use in Galaxy current
- 17:4517:45, 13 September 2011 diff hist +265 UAB Galaxy Workshop Tutorial →Getting data into Galaxy
- 17:1217:12, 13 September 2011 diff hist +811 UAB Galaxy Workshop Tutorial →UAB Galaxy DNA-Seq Step-by-Step Tutorial
- 16:4816:48, 13 September 2011 diff hist +19 UAB Galaxy Workshop Tutorial →Overview: Mention workflows
- 16:4416:44, 13 September 2011 diff hist +523 N UAB Galaxy Workshop Tutorial Creation of page
- 16:1216:12, 13 September 2011 diff hist +8 Galaxy Moving tutorials to a separate page
12 September 2011
- 19:5219:52, 12 September 2011 diff hist +406 Galaxy Structure for Tutorial started
8 September 2011
- 16:4716:47, 8 September 2011 diff hist +55 2011 HPC Boot Camp Adding section on logging in and uploading data to galaxy
- 16:2016:20, 8 September 2011 diff hist +9 m Galaxy SRMA mention
- 15:5815:58, 8 September 2011 diff hist 0 m Galaxy Typo
- 15:5715:57, 8 September 2011 diff hist −1,279 Galaxy Major overhaul, added script for updating indices
7 September 2011
- 21:4621:46, 7 September 2011 diff hist +1,817 Galaxy Added bash script
25 August 2011
- 21:3421:34, 25 August 2011 diff hist +549 Galaxy →Adding Novel Datasets
- 21:3021:30, 25 August 2011 diff hist +1,229 Galaxy →Adding Novel Datasets
- 21:1621:16, 25 August 2011 diff hist +15 Galaxy →Adding Novel Datasets
- 21:1121:11, 25 August 2011 diff hist +136 Galaxy →Adding Novel Datasets
- 21:0721:07, 25 August 2011 diff hist +701 Galaxy →Datasets
- 18:0718:07, 25 August 2011 diff hist +212 Galaxy →BWA Indices
- 18:0218:02, 25 August 2011 diff hist +2 Galaxy →Sam and FAIDX indices
- 18:0218:02, 25 August 2011 diff hist +36 Galaxy →BWA Indices
- 18:0118:01, 25 August 2011 diff hist +178 Galaxy →Datasets
- 17:5617:56, 25 August 2011 diff hist +1,121 Galaxy →Datasets
- 17:2917:29, 25 August 2011 diff hist +125 Galaxy →Datasets
- 16:0816:08, 25 August 2011 diff hist +321 Galaxy →Directory Creation
- 15:0615:06, 25 August 2011 diff hist +737 Galaxy Additional information about setting up a new dataset
12 May 2011
- 15:3815:38, 12 May 2011 diff hist −2,970 Galaxy Removed Cheaha Iinstallation Information, now on own wiki
11 May 2011
- 19:3119:31, 11 May 2011 diff hist +44 Galaxy →Next Gen Sequencing Software (order of install on "cheaha"): Top Hat
9 May 2011
- 21:3321:33, 9 May 2011 diff hist +92 m Galaxy →Next Gen Sequencing Software (order of install on "cheaha")
- 21:3021:30, 9 May 2011 diff hist +165 Galaxy →Next Gen Sequencing Software (order of install on "cheaha"): velevet
- 20:5620:56, 9 May 2011 diff hist +262 Galaxy Added section for NextGen indices
- 20:0720:07, 9 May 2011 diff hist +341 Galaxy →Next Gen Sequencing Software (order of install on "cheaha"): srma
- 19:5719:57, 9 May 2011 diff hist +64 Galaxy →Next Gen Sequencing Software (order of install on "cheaha")
- 19:5619:56, 9 May 2011 diff hist +169 Galaxy →Next Gen Sequencing Software (order of install on "cheaha")
- 19:2519:25, 9 May 2011 diff hist +117 m Galaxy →Next Gen Sequencing Software (order of install on "cheaha")
- 19:0919:09, 9 May 2011 diff hist +317 Galaxy →Next Gen Sequencing Software (order of install on "cheaha")
- 18:1418:14, 9 May 2011 diff hist +120 Galaxy →Next Gen Sequencing Software (order of install on "cheaha")
- 18:0518:05, 9 May 2011 diff hist +283 Galaxy →Next Gen Sequencing Software
6 May 2011
- 22:1722:17, 6 May 2011 diff hist +96 Galaxy →Next Gen Sequencing Software
5 May 2011
- 21:4021:40, 5 May 2011 diff hist +122 m Galaxy →Next Gen Sequencing Software
- 21:3421:34, 5 May 2011 diff hist +732 Galaxy →Cheaha Cluster Installation Setup Notes
- 21:2821:28, 5 May 2011 diff hist +34 m Galaxy Adding Cheaha Setup Info, reordering hierarchy
1 March 2011
- 19:5519:55, 1 March 2011 diff hist +379 Galaxy Redesign to make things more consistent
- 19:4619:46, 1 March 2011 diff hist +17 m Galaxy No edit summary
- 19:4519:45, 1 March 2011 diff hist +306 Galaxy SNPeff
25 February 2011
- 22:4522:45, 25 February 2011 diff hist +547 Galaxy GNU Plot problems with Galaxy VM
- 22:4122:41, 25 February 2011 diff hist +116 Galaxy →Temporary Directory and the $TEMP variable
23 February 2011
- 21:0021:00, 23 February 2011 diff hist +165 Galaxy LD_LIBRARY_PATH for samtools
16 February 2011
- 23:2523:25, 16 February 2011 diff hist +297 Galaxy Temporary directory and $TEMP variable
- 22:4622:46, 16 February 2011 diff hist −173 Galaxy →Post Processing: Makefile fix
- 22:3722:37, 16 February 2011 diff hist +973 Galaxy →Post Processing: Fix using gzopen64 contaiing zlib
- 20:5520:55, 16 February 2011 diff hist +281 Galaxy →Post Processing: gzopen64 on ubuntu version of zlib
- 20:4220:42, 16 February 2011 diff hist +86 m Galaxy removing zlib-devel
- 20:3920:39, 16 February 2011 diff hist +222 Galaxy →Post Processing: Removing duplicate zlibs
15 February 2011
- 22:5422:54, 15 February 2011 diff hist +882 Galaxy →Post Processing: SAML problems
- 22:4622:46, 15 February 2011 diff hist +101 Galaxy megablast info
- 22:3322:33, 15 February 2011 diff hist +105 Galaxy No edit summary
- 22:3022:30, 15 February 2011 diff hist +86 Galaxy No edit summary
- 22:1822:18, 15 February 2011 diff hist +97 Galaxy No edit summary
- 21:4421:44, 15 February 2011 diff hist +84 m Galaxy No edit summary
- 21:3621:36, 15 February 2011 diff hist +467 Galaxy No edit summary
- 20:3520:35, 15 February 2011 diff hist +259 m Galaxy No edit summary
- 20:2020:20, 15 February 2011 diff hist +273 m Galaxy No edit summary
- 19:4919:49, 15 February 2011 diff hist +722 Galaxy →RPy, R, Atlas, Numpy, BLAS, LAPACK
14 February 2011
- 23:2123:21, 14 February 2011 diff hist +372 Galaxy No edit summary
7 February 2011
- 23:0123:01, 7 February 2011 diff hist +354 Galaxy Bugs
- 21:0921:09, 7 February 2011 diff hist +157 Galaxy Added link for mercurial setup
3 February 2011
- 22:0522:05, 3 February 2011 diff hist +292 Galaxy No edit summary
27 January 2011
- 22:1622:16, 27 January 2011 diff hist +706 Galaxy Adding shib configuration for galaxy
13 January 2011
- 21:5421:54, 13 January 2011 diff hist +183 m Galaxy SMTP
- 20:5820:58, 13 January 2011 diff hist +134 m Galaxy selinux enforcement policy change
- 20:5020:50, 13 January 2011 diff hist +254 m Galaxy No edit summary
6 January 2011
- 22:5722:57, 6 January 2011 diff hist +645 Galaxy Apache and Postgres additions