source: other/pipeline/trunk

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Diff Rev Age Author Log Message
(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) @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) @4045   7 years Nicklas Nordborg References #901: Set multiple paths for run-archive Updated the …
(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.
(add) @2383   9 years Nicklas Nordborg Creating trunk and tags folder for the pipeline project.
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