User contributions
From UABgrid Documentation
(Latest | Earliest) View (newer 500 | older 500) (20 | 50 | 100 | 250 | 500)
- 15:14, 15 September 2011 (diff | hist) . . (+41) . . Galaxy DNA-Seq Tutorial (→Pileup)
- 15:14, 15 September 2011 (diff | hist) . . (0) . . N File:GalaxyTutorialSharedLibrary.jpg (top)
- 15:13, 15 September 2011 (diff | hist) . . (+209) . . Galaxy DNA-Seq Tutorial (→Pileup)
- 14:56, 15 September 2011 (diff | hist) . . (+26) . . Galaxy DNA-Seq Tutorial (→Pileup)
- 14:56, 15 September 2011 (diff | hist) . . (+44) . . Galaxy DNA-Seq Tutorial (→BAM Conversion)
- 14:54, 15 September 2011 (diff | hist) . . (+573) . . Galaxy DNA-Seq Tutorial (→BAM Conversion)
- 14:44, 15 September 2011 (diff | hist) . . (+285) . . Galaxy DNA-Seq Tutorial
- 14:32, 15 September 2011 (diff | hist) . . (+106) . . Galaxy DNA-Seq Tutorial (→Other Variant Detection Approaches)
- 14:28, 15 September 2011 (diff | hist) . . (-2) . . Galaxy DNA-Seq Tutorial (→Samtools)
- 14:28, 15 September 2011 (diff | hist) . . (+116) . . Galaxy DNA-Seq Tutorial (→Variant Analysis)
- 14:09, 15 September 2011 (diff | hist) . . (+75) . . Galaxy DNA-Seq Tutorial
- 14:06, 15 September 2011 (diff | hist) . . (+16) . . N File:SamBamFileFormatFlags.jpg (SAM format flags) (top)
- 14:02, 15 September 2011 (diff | hist) . . (+45) . . Galaxy DNA-Seq Tutorial
- 13:56, 15 September 2011 (diff | hist) . . (+153) . . Galaxy DNA-Seq Tutorial (→BAM Conversion)
- 13:51, 15 September 2011 (diff | hist) . . (+237) . . Galaxy DNA-Seq Tutorial (→Short read alignment to reference genome using BWA)
- 13:46, 15 September 2011 (diff | hist) . . (+152) . . Galaxy DNA-Seq Tutorial (→Results)
- 13:43, 15 September 2011 (diff | hist) . . (+262) . . Galaxy DNA-Seq Tutorial (→Performing cleanup)
- 13:40, 15 September 2011 (diff | hist) . . (+32) . . N File:FastQTrimmerRun.jpg (CMV 21950R being trimmed from 3') (top)
- 13:31, 15 September 2011 (diff | hist) . . (+226) . . Galaxy DNA-Seq Tutorial
- 13:27, 15 September 2011 (diff | hist) . . (+88) . . Galaxy DNA-Seq Tutorial (→Quality Statistics and Boxplot)
- 13:25, 15 September 2011 (diff | hist) . . (0) . . File:DrawQualityScoreBoxplot.jpg (uploaded a new version of "File:DrawQualityScoreBoxplot.jpg": Run box plot) (top)
- 13:22, 15 September 2011 (diff | hist) . . (+35) . . Galaxy DNA-Seq Tutorial (→Quality Statistics and Boxplot)
- 13:21, 15 September 2011 (diff | hist) . . (0) . . N File:QualityStatsResults.jpg (top)
- 13:18, 15 September 2011 (diff | hist) . . (-10) . . Galaxy DNA-Seq Tutorial (→Quality Statistics and Boxplot)
- 13:17, 15 September 2011 (diff | hist) . . (0) . . N File:RunComputeQualityStats.jpg (top)
- 13:14, 15 September 2011 (diff | hist) . . (+30) . . Galaxy DNA-Seq Tutorial
- 13:11, 15 September 2011 (diff | hist) . . (+98) . . Galaxy DNA-Seq Tutorial (→Reference Genome)
- 13:09, 15 September 2011 (diff | hist) . . (+114) . . Galaxy DNA-Seq Tutorial
- 13:04, 15 September 2011 (diff | hist) . . (+465) . . Galaxy DNA-Seq Tutorial (FastQC and Compute stats cleanup)
- 12:47, 15 September 2011 (diff | hist) . . (0) . . N File:FastQCRunSettings.jpg (top)
- 12:39, 15 September 2011 (diff | hist) . . (+127) . . Galaxy DNA-Seq Tutorial
- 12:32, 15 September 2011 (diff | hist) . . (+115) . . Galaxy DNA-Seq Tutorial (→Reference Genome)
- 12:30, 15 September 2011 (diff | hist) . . (+217) . . Galaxy (→Available datasets: Added new datasets)
- 12:21, 15 September 2011 (diff | hist) . . (+368) . . Galaxy DNA-Seq Tutorial
- 12:09, 15 September 2011 (diff | hist) . . (+66) . . Galaxy DNA-Seq Tutorial (→Linking to data)
- 12:08, 15 September 2011 (diff | hist) . . (0) . . N File:DataLibraryVacWRFastQ.jpg (top)
- 09:56, 15 September 2011 (diff | hist) . . (+38) . . Galaxy DNA-Seq Tutorial (Pileup filtering)
- 09:55, 15 September 2011 (diff | hist) . . (+35) . . N File:PileupFiltering100Reads.jpg (Pileup run settings for Vaccinia WR) (top)
- 23:13, 14 September 2011 (diff | hist) . . (+75) . . Galaxy DNA-Seq Tutorial (Filtering SNPs)
- 23:11, 14 September 2011 (diff | hist) . . (+50) . . N File:FilterRunVacWR.jpg (How to filter a SAM file for SNPs versus reference) (top)
- 22:22, 14 September 2011 (diff | hist) . . (+32) . . Galaxy DNA-Seq Tutorial
- 22:21, 14 September 2011 (diff | hist) . . (+27) . . N File:SNPEffResults.jpg (SNP Results for Vaccinia WR) (top)
- 22:20, 14 September 2011 (diff | hist) . . (+141) . . Galaxy DNA-Seq Tutorial
- 22:18, 14 September 2011 (diff | hist) . . (+17) . . N File:SNPEffCoverage.jpg (For a vaccinia WR) (top)
- 22:17, 14 September 2011 (diff | hist) . . (+214) . . Galaxy DNA-Seq Tutorial (SNPEff separate section)
- 21:47, 14 September 2011 (diff | hist) . . (+78) . . Galaxy DNA-Seq Tutorial (→Variant Analysis)
- 21:45, 14 September 2011 (diff | hist) . . (+19) . . N File:SNPEff.jpg (SNPEff run settings) (top)
- 21:38, 14 September 2011 (diff | hist) . . (+127) . . Galaxy DNA-Seq Tutorial (→BAM Conversion)
- 21:34, 14 September 2011 (diff | hist) . . (+153) . . Galaxy DNA-Seq Tutorial (→Variant Analysis)
- 21:09, 14 September 2011 (diff | hist) . . (+107) . . Galaxy DNA-Seq Tutorial (→Variant Analysis)
- 21:08, 14 September 2011 (diff | hist) . . (+44) . . N File:GeneratePileup.jpg (Generate pileup for Vaccinia, call consensus) (top)
- 21:06, 14 September 2011 (diff | hist) . . (+20) . . Galaxy DNA-Seq Tutorial (→Looking at differences with SNPEff)
- 16:36, 14 September 2011 (diff | hist) . . (+22) . . Galaxy DNA-Seq Tutorial (Flagstat)
- 16:35, 14 September 2011 (diff | hist) . . (+29) . . N File:Sam2bam.jpg (Conversion of SAM file to BAM) (top)
- 16:35, 14 September 2011 (diff | hist) . . (+44) . . Galaxy DNA-Seq Tutorial (Flagstat)
- 16:35, 14 September 2011 (diff | hist) . . (+22) . . N File:Flagstat.jpg (Flag stat on BAM files) (top)
- 15:53, 14 September 2011 (diff | hist) . . (-1) . . Galaxy DNA-Seq Tutorial (→Short read alignment to reference genome using BWA)
- 15:52, 14 September 2011 (diff | hist) . . (+26) . . N File:Bwa run cmv 227r.jpg (BWA run of VAC WR CMV 227R) (top)
- 15:33, 14 September 2011 (diff | hist) . . (+31) . . Galaxy DNA-Seq Tutorial (→Short read alignment to reference genome using BWA)
- 15:33, 14 September 2011 (diff | hist) . . (+39) . . N File:Bwa run cmv 21950r.jpg (Running BWA on CMV 21950R in UAB Galaxy) (top)
- 15:08, 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") (top)
- 15:05, 14 September 2011 (diff | hist) . . (+38) . . Galaxy DNA-Seq Tutorial (→Assessing the quality of the data)
- 15:04, 14 September 2011 (diff | hist) . . (0) . . N File:DrawQualityScoreBoxplot.jpg
- 14:59, 14 September 2011 (diff | hist) . . (+44) . . Galaxy DNA-Seq Tutorial (→Performing cleanup)
- 14:58, 14 September 2011 (diff | hist) . . (+47) . . N File:Cmv21950r 3 1 trimmed boxplot.jpg (CMV 21950R after trimming one base off the end.) (top)
- 14:33, 14 September 2011 (diff | hist) . . (+43) . . Galaxy DNA-Seq Tutorial (Adding pre-trim boxplot)
- 14:32, 14 September 2011 (diff | hist) . . (+49) . . N File:Cmv21950r 3 1 original boxplot.jpg (Original boxplot before trimming of Vac WR 21950R)
- 14:27, 14 September 2011 (diff | hist) . . (+49) . . Galaxy DNA-Seq Tutorial (Adding computation of qualitys stats)
- 14:25, 14 September 2011 (diff | hist) . . (+45) . . N File:ComputeQualityStatsCMV21950R 3 1.jpg (Image of running computation of quality stats) (top)
- 16:34, 13 September 2011 (diff | hist) . . (+212) . . Galaxy DNA-Seq Tutorial (→Assessing the quality of the data)
- 16:31, 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) (top)
- 16:30, 13 September 2011 (diff | hist) . . (+396) . . Galaxy DNA-Seq Tutorial (→Assessing the quality of the data)
- 15:46, 13 September 2011 (diff | hist) . . (+619) . . Galaxy DNA-Seq Tutorial (Formatting data)
- 15:31, 13 September 2011 (diff | hist) . . (+70) . . N File:DataType.jpg (Data attributes for a vaccinia virus fastq file from the history pane.) (top)
- 15:29, 13 September 2011 (diff | hist) . . (+362) . . Galaxy DNA-Seq Tutorial (→Linking to data)
- 15:26, 13 September 2011 (diff | hist) . . (+66) . . N File:HistoryPane.jpg (What your history pane should look like after linking in the data.) (top)
- 13:34, 13 September 2011 (diff | hist) . . (+437) . . Galaxy DNA-Seq Tutorial (Linking in WR data)
- 13:05, 13 September 2011 (diff | hist) . . (+219) . . UAB Galaxy Workshop Tutorial
- 13:01, 13 September 2011 (diff | hist) . . (-48) . . UAB Galaxy Workshop Tutorial
- 12:57, 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...")
- 12:55, 13 September 2011 (diff | hist) . . (-243) . . UAB Galaxy Workshop Tutorial (Moving DNA-Seq and RNA-Seq to their own pages)
- 11:59, 13 September 2011 (diff | hist) . . (+123) . . UAB Galaxy Workshop Tutorial (→Getting data into Galaxy: Added links to data uploading, still need cleanup.)
- 11:54, 13 September 2011 (diff | hist) . . (+36) . . UploadLargeData (Added image)
- 11:51, 13 September 2011 (diff | hist) . . (+57) . . N File:UploadLinkDataFilesGUI.jpg (Picture of linking in directory of files to use in Galaxy) (top)
- 11:45, 13 September 2011 (diff | hist) . . (+265) . . UAB Galaxy Workshop Tutorial (→Getting data into Galaxy)
- 11:12, 13 September 2011 (diff | hist) . . (+811) . . UAB Galaxy Workshop Tutorial (→UAB Galaxy DNA-Seq Step-by-Step Tutorial)
- 10:48, 13 September 2011 (diff | hist) . . (+19) . . UAB Galaxy Workshop Tutorial (→Overview: Mention workflows)
- 10:44, 13 September 2011 (diff | hist) . . (+523) . . N UAB Galaxy Workshop Tutorial (Creation of page)
- 10:12, 13 September 2011 (diff | hist) . . (+8) . . Galaxy (Moving tutorials to a separate page)
- 13:52, 12 September 2011 (diff | hist) . . (+406) . . Galaxy (Structure for Tutorial started)
- 10:47, 8 September 2011 (diff | hist) . . (+55) . . 2011 HPC Boot Camp (Adding section on logging in and uploading data to galaxy)
- 10:20, 8 September 2011 (diff | hist) . . (+9) . . m Galaxy (SRMA mention)
- 09:58, 8 September 2011 (diff | hist) . . (0) . . m Galaxy (Typo)
- 09:57, 8 September 2011 (diff | hist) . . (-1,279) . . Galaxy (Major overhaul, added script for updating indices)
- 15:46, 7 September 2011 (diff | hist) . . (+1,817) . . Galaxy (Added bash script)
- 15:34, 25 August 2011 (diff | hist) . . (+549) . . Galaxy (→Adding Novel Datasets)
- 15:30, 25 August 2011 (diff | hist) . . (+1,229) . . Galaxy (→Adding Novel Datasets)
- 15:16, 25 August 2011 (diff | hist) . . (+15) . . Galaxy (→Adding Novel Datasets)
- 15:11, 25 August 2011 (diff | hist) . . (+136) . . Galaxy (→Adding Novel Datasets)
- 15:07, 25 August 2011 (diff | hist) . . (+701) . . Galaxy (→Datasets)
- 12:07, 25 August 2011 (diff | hist) . . (+212) . . Galaxy (→BWA Indices)
- 12:02, 25 August 2011 (diff | hist) . . (+2) . . Galaxy (→Sam and FAIDX indices)
- 12:02, 25 August 2011 (diff | hist) . . (+36) . . Galaxy (→BWA Indices)
- 12:01, 25 August 2011 (diff | hist) . . (+178) . . Galaxy (→Datasets)
- 11:56, 25 August 2011 (diff | hist) . . (+1,121) . . Galaxy (→Datasets)
- 11:29, 25 August 2011 (diff | hist) . . (+125) . . Galaxy (→Datasets)
- 10:08, 25 August 2011 (diff | hist) . . (+321) . . Galaxy (→Directory Creation)
- 09:06, 25 August 2011 (diff | hist) . . (+737) . . Galaxy (Additional information about setting up a new dataset)
- 09:38, 12 May 2011 (diff | hist) . . (-2,970) . . Galaxy (Removed Cheaha Iinstallation Information, now on own wiki)
- 13:31, 11 May 2011 (diff | hist) . . (+44) . . Galaxy (→Next Gen Sequencing Software (order of install on "cheaha"): Top Hat)
- 15:33, 9 May 2011 (diff | hist) . . (+92) . . m Galaxy (→Next Gen Sequencing Software (order of install on "cheaha"))
- 15:30, 9 May 2011 (diff | hist) . . (+165) . . Galaxy (→Next Gen Sequencing Software (order of install on "cheaha"): velevet)
- 14:56, 9 May 2011 (diff | hist) . . (+262) . . Galaxy (Added section for NextGen indices)
- 14:07, 9 May 2011 (diff | hist) . . (+341) . . Galaxy (→Next Gen Sequencing Software (order of install on "cheaha"): srma)
- 13:57, 9 May 2011 (diff | hist) . . (+64) . . Galaxy (→Next Gen Sequencing Software (order of install on "cheaha"))
- 13:56, 9 May 2011 (diff | hist) . . (+169) . . Galaxy (→Next Gen Sequencing Software (order of install on "cheaha"))
- 13:25, 9 May 2011 (diff | hist) . . (+117) . . m Galaxy (→Next Gen Sequencing Software (order of install on "cheaha"))
- 13:09, 9 May 2011 (diff | hist) . . (+317) . . Galaxy (→Next Gen Sequencing Software (order of install on "cheaha"))
- 12:14, 9 May 2011 (diff | hist) . . (+120) . . Galaxy (→Next Gen Sequencing Software (order of install on "cheaha"))
- 12:05, 9 May 2011 (diff | hist) . . (+283) . . Galaxy (→Next Gen Sequencing Software)
- 16:17, 6 May 2011 (diff | hist) . . (+96) . . Galaxy (→Next Gen Sequencing Software)
- 15:40, 5 May 2011 (diff | hist) . . (+122) . . m Galaxy (→Next Gen Sequencing Software)
- 15:34, 5 May 2011 (diff | hist) . . (+732) . . Galaxy (→Cheaha Cluster Installation Setup Notes)
- 15:28, 5 May 2011 (diff | hist) . . (+34) . . m Galaxy (Adding Cheaha Setup Info, reordering hierarchy)
- 13:55, 1 March 2011 (diff | hist) . . (+379) . . Galaxy (Redesign to make things more consistent)
- 13:46, 1 March 2011 (diff | hist) . . (+17) . . m Galaxy
- 13:45, 1 March 2011 (diff | hist) . . (+306) . . Galaxy (SNPeff)
- 16:45, 25 February 2011 (diff | hist) . . (+547) . . Galaxy (GNU Plot problems with Galaxy VM)
- 16:41, 25 February 2011 (diff | hist) . . (+116) . . Galaxy (→Temporary Directory and the $TEMP variable)
- 15:00, 23 February 2011 (diff | hist) . . (+165) . . Galaxy (LD_LIBRARY_PATH for samtools)
- 17:25, 16 February 2011 (diff | hist) . . (+297) . . Galaxy (Temporary directory and $TEMP variable)
- 16:46, 16 February 2011 (diff | hist) . . (-173) . . Galaxy (→Post Processing: Makefile fix)
- 16:37, 16 February 2011 (diff | hist) . . (+973) . . Galaxy (→Post Processing: Fix using gzopen64 contaiing zlib)
- 14:55, 16 February 2011 (diff | hist) . . (+281) . . Galaxy (→Post Processing: gzopen64 on ubuntu version of zlib)
- 14:42, 16 February 2011 (diff | hist) . . (+86) . . m Galaxy (removing zlib-devel)
- 14:39, 16 February 2011 (diff | hist) . . (+222) . . Galaxy (→Post Processing: Removing duplicate zlibs)
- 16:54, 15 February 2011 (diff | hist) . . (+882) . . Galaxy (→Post Processing: SAML problems)
- 16:46, 15 February 2011 (diff | hist) . . (+101) . . Galaxy (megablast info)
- 16:33, 15 February 2011 (diff | hist) . . (+105) . . Galaxy
- 16:30, 15 February 2011 (diff | hist) . . (+86) . . Galaxy
- 16:18, 15 February 2011 (diff | hist) . . (+97) . . Galaxy
- 15:44, 15 February 2011 (diff | hist) . . (+84) . . m Galaxy
- 15:36, 15 February 2011 (diff | hist) . . (+467) . . Galaxy
- 14:35, 15 February 2011 (diff | hist) . . (+259) . . m Galaxy
- 14:20, 15 February 2011 (diff | hist) . . (+273) . . m Galaxy
- 13:49, 15 February 2011 (diff | hist) . . (+722) . . Galaxy (→RPy, R, Atlas, Numpy, BLAS, LAPACK)
- 17:21, 14 February 2011 (diff | hist) . . (+372) . . Galaxy
- 17:01, 7 February 2011 (diff | hist) . . (+354) . . Galaxy (Bugs)
- 15:09, 7 February 2011 (diff | hist) . . (+157) . . Galaxy (Added link for mercurial setup)
- 16:05, 3 February 2011 (diff | hist) . . (+292) . . Galaxy
- 16:16, 27 January 2011 (diff | hist) . . (+706) . . Galaxy (Adding shib configuration for galaxy)
- 15:54, 13 January 2011 (diff | hist) . . (+183) . . m Galaxy (SMTP)
- 14:58, 13 January 2011 (diff | hist) . . (+134) . . m Galaxy (selinux enforcement policy change)
- 14:50, 13 January 2011 (diff | hist) . . (+254) . . m Galaxy
- 16:57, 6 January 2011 (diff | hist) . . (+645) . . Galaxy (Apache and Postgres additions)
(Latest | Earliest) View (newer 500 | older 500) (20 | 50 | 100 | 250 | 500)
