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Diff Rev Age Author Log Message
(edit) @6521   22 months Nicklas Nordborg Adding a wrapper for calling Hisat 2.2. It requries extra entries in …
(edit) @6419   2 years Nicklas Nordborg References #1335: Calculate average read length in FASTQ files after …
(edit) @6378   2 years Nicklas Nordborg Fixes #1325: Calculating the average fragment size needs fixing due to …
(edit) @5934   3 years Nicklas Nordborg References #1243: Improve status checking for NovaSeq? Updated the …
(edit) @5856   4 years Nicklas Nordborg References #1231: Add support for sequencing with NovaSeq? Added …
(edit) @5842   4 years Nicklas Nordborg References #1218: Implement MIPs alignment Added functions for …
(edit) @5840   4 years Nicklas Nordborg References #1218: Implement MIPs alignment Added functions for …
(edit) @5838   4 years Nicklas Nordborg References #1218: Implement MIPs alignment Added functions for the …
(edit) @5836   4 years Nicklas Nordborg References #1218: Implement MIPs alignment Added functions for …
(edit) @5834   4 years Nicklas Nordborg References #1218: Implement MIPs alignment Started to implement a …
(edit) @5825   4 years Jari Häkkinen Change needed to find R's BLAS/LAPACK implementation
(edit) @5810   4 years Nicklas Nordborg References #1222: Remove the G5 distance calculations from the variant …
(edit) @5807   4 years Nicklas Nordborg References #1215: Include mutation signature analysis in the variant …
(edit) @5796   4 years Nicklas Nordborg References #1215: Include mutation signature analysis in the variant …
(edit) @5771   4 years Nicklas Nordborg References #1208: Implement wizard for building database of variant …
(edit) @5769   4 years Nicklas Nordborg References #1208: Implement wizard for building database of variant …
(edit) @5767   4 years Nicklas Nordborg References #1208: Implement wizard for building database of variant …
(edit) @5753   4 years Nicklas Nordborg References #1205: Variant calling fails with "malformed BED entry" …
(edit) @5747   4 years Nicklas Nordborg Fixes an issue with missing "N" values in the lookup tables for GC …
(edit) @5719   4 years Nicklas Nordborg References #1199: Implement Variant calling pipeline Added …
(edit) @5718   4 years Nicklas Nordborg References #1199: Implement Variant calling pipeline Helper script …
(edit) @5712   4 years Nicklas Nordborg References #1199: Implement Variant calling pipeline Added helper …
(edit) @5709   4 years Nicklas Nordborg References #1199: Implement Variant calling pipeline Added python …
(edit) @5698   4 years Nicklas Nordborg References #1199: Implement Variant calling pipeline Added wrapper …
(edit) @5610   4 years Jari Häkkinen removed obsolete script
(edit) @5589   4 years Nicklas Nordborg References #1146: Demux for the MIPs pipeline Added fqpaste.pl to the …
(edit) @5529   4 years Nicklas Nordborg References #1161: Update picard to 2.20 Adding the picard2 wrapper …
(edit) @5476   4 years Nicklas Nordborg References #1142: Create MIPs flow cell and start sequencing Updated …
(edit) @5474   4 years Nicklas Nordborg References #1142: Create MIPs flow cell and start sequencing Added a …
(edit) @4766   5 years Nicklas Nordborg Changes for future release IncaXML2CSV 1.3
(edit) @4765   5 years Nicklas Nordborg Tagging IncaXML2CSV 1.2
(edit) @4764   5 years Nicklas Nordborg Preparing to release IncaXML2CSV 1.2
(edit) @4709   6 years Nicklas Nordborg References #1021: Add INCA 2.0 columns to the blacklist Added: * …
(edit) @4589   6 years Nicklas Nordborg References #997: Implement new secondary analysis pipeline Updated …
(edit) @4566   6 years Nicklas Nordborg References #983: Merge the Tophat alignment and Cufflinks job to a …
(edit) @4194   7 years Nicklas Nordborg Preparations for future release of INCA XML to CSV converter 1.2
(edit) @4193   7 years Nicklas Nordborg Tagging INCA XML to CSV converter 1.1
(edit) @4192   7 years Nicklas Nordborg Preparing to release INCA XML to CSV converter 1.1
(edit) @4191   7 years Nicklas Nordborg Fixes #914: Add more columns to the blacklist Blacklisted columns now …
(edit) @4045   7 years Nicklas Nordborg References #901: Set multiple paths for run-archive Updated the …
(edit) @3966   7 years Nicklas Nordborg Changes for future release IncaXml2Csv 1.1
(edit) @3965   7 years Nicklas Nordborg Tagging IncaXml2Csv 1.0
(edit) @3964   7 years Nicklas Nordborg Preparing to release IncaXml2Csv 1.0.
(edit) @3898   7 years Nicklas Nordborg References #881: Implement INCA XML to CSV converter Changes to make …
(edit) @3897   7 years Nicklas Nordborg References #881: Implement INCA XML to CSV converter Changes to make …
(edit) @3896   7 years Nicklas Nordborg References #881: Implement INCA XML to CSV converter Updated README …
(edit) @3894   7 years Nicklas Nordborg References #881: Implement INCA XML to CSV converter Arrgggh... …
(edit) @3893   7 years Nicklas Nordborg References #881: Implement INCA XML to CSV converter Ignore the new …
(edit) @3892   7 years Nicklas Nordborg References #881: Implement INCA XML to CSV converter Renamed JAR/TAR …
(edit) @3891   7 years Nicklas Nordborg References #881: Implement INCA XML to CSV converter Personal number …
(edit) @3890   7 years Nicklas Nordborg References #881: Implement INCA XML to CSV converter Added "Save as" …
(edit) @3887   7 years Nicklas Nordborg References #881: Implement INCA XML to CSV converter Added a writer …
(edit) @3885   7 years Nicklas Nordborg References #881: Implement INCA XML to CSV converter Added a SAX …
(edit) @3884   7 years Nicklas Nordborg References #881: Implement INCA XML to CSV converter Open a file …
(edit) @3883   7 years Nicklas Nordborg References #881: Implement INCA XML to CSV converter Added parser for …
(edit) @3881   7 years Nicklas Nordborg References #881: Implement INCA XML to CSV converter Added * Folder …
(edit) @3880   7 years Nicklas Nordborg Creating space for the new INCA XML to CSV converter project.
(edit) @3879   7 years Nicklas Nordborg Creating space for the new INCA XML to CSV converter project.
(edit) @3698   8 years Nicklas Nordborg Adding nextseq_status.sh script for checking the status of a NextSeq? …
(edit) @3589   8 years Jari Häkkinen Restoring svn:eol-style to LF
(edit) @3586   8 years Jari Häkkinen Fixing svn:eol-style
(edit) @3585   8 years Jari Häkkinen Updating post-alingment script to latest released version. The script …
(edit) @3584   8 years Jari Häkkinen Fixing svndigest&svncopyright properties
(edit) @3583   8 years Jari Häkkinen Fixing Id keyword
(edit) @3099   9 years Nicklas Nordborg Updating Picard wrapper script to make it compatible with Picard 1.128 …
(edit) @2852   9 years Nicklas Nordborg Ignore .project file from Eclipse.
(edit) @2831   9 years Jari Häkkinen New version from Christian. added proper argument/option handling; …
(edit) @2830   9 years Jari Häkkinen Print integers as integers.
(edit) @2786   9 years Nicklas Nordborg References #653: Use explicit paths to all important program used in …
(edit) @2749   9 years Nicklas Nordborg Adding script for replacing tracking_id values in the fpkm_tracking …
(edit) @2696   9 years Nicklas Nordborg Adding script for fixing the unmapped.bam file generated by tophat so …
(edit) @2679   9 years Nicklas Nordborg Adding script for calculating average of fragment lengths.
(edit) @2567   9 years Nicklas Nordborg Removing scripts that are no longer used by reggie.
(edit) @2558   9 years Nicklas Nordborg Forgot to execute the last samtools command
(edit) @2557   9 years Nicklas Nordborg Added 'alignment_statisics.sh' which replaces the …
(edit) @2537   9 years Nicklas Nordborg Adding wrapper script for directing output to stderr or stdout …
(edit) @2496   9 years Nicklas Nordborg Adding svn properties
(edit) @2495   9 years Nicklas Nordborg Adding wrapper for calling trimmomatic. Includes default settings for …
(edit) @2442   9 years Nicklas Nordborg Check enironment variable PicardMemory? for amount of memory to give to …
(edit) @2430   9 years Nicklas Nordborg Switched from illumina2bam_wrapper to picard for demultiplexing. …
(edit) @2421   9 years Nicklas Nordborg Renamed the 'filtered' step to 'masked'. See …
(edit) @2413   9 years Nicklas Nordborg Remove 'filter_' prefix in the PE_filter script.
(edit) @2398   9 years Nicklas Nordborg Adding statistics_tophat.sh
(edit) @2396   9 years Nicklas Nordborg Adding tophat_single.sh and sync_resyltfiles.sh scrips. tophat_single …
(edit) @2393   9 years Nicklas Nordborg Adding PE_filter.sh script. Changes from original script is that …
(edit) @2387   9 years Nicklas Nordborg Scripts used for the demux and merge steps in reggie.
(edit) @2383   9 years Nicklas Nordborg Creating trunk and tags folder for the pipeline project.
(edit) @2382   9 years Nicklas Nordborg Creating root folder for the 'pipeline' scripts.
(add) @2381   9 years Nicklas Nordborg Adding folder for other projects.
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