Updated by Jelena - 15:00 08/Jun/2017

CC4 release - launched 15/Mar/2016

Bug fixes and updates in CCanalyser4.pl (after release) :

  • 26/Sep/2016 Bug fix - The sam-->bam transform in the end of pipe made zero-size files for the convenience files "CAPTURE" and "ALL READS" (combined files for all capture sites), as sam heading was missing (see below). Now fixed.
  • 01/Apr/2016 Typo fix - Corrected the duplicate filter counter name to be 16 instead of 6 (gets now printed to correct spot in the output log file).

    • Bug fixes and updates in Pipe2/pipe.sh (after release) :

  • 08/Jun/2017 Added feature - Added bowtie1 parameter -v ( to allow the "wished amount of mismatches within the whole read" while ignoring quality scores for those mismatched bases ) .
  • 25/May/2017 Added feature - Added disk usage checkpoints for fastq combining and iterative mapping steps (to better catch situations where user runs out of quota during the run) .
  • 06/Jan/2017 Bug fix - Fixed the NlaIII/DpnII python plot counts fix from 24/Oct/2016 (were still not reported properly).
  • 24/Oct/2016 Bug fix - The blat-filtered fragments locations were not given out properly (generated empty file). Now fixed.
  • 24/Oct/2016 Bug fix - Fixed the NlaIII counts in python plot (were not reported properly in 11Oct update).
  • 24/Oct/2016 Improved feature - Set all output hub tracks to "hide" by default.
  • 11/Oct/2016 Added feature - Restriction enzyme nlaIII is now fully supported. DpnII is still the default. Specify with --dnp and --nla .
  • 11/Oct/2016 Added feature - To make multiple runs with same oligo file faster : added flag --BLATforREUSEfolderPath to run using READY-MADE blat filter files (from a previous run). (see /t1-data/data/hugheslab/jelenatools/CC/CC4/Pipe2/pipe.sh --help for instructions)
  • 28/Sep/2016 Added feature - Added support to danRer10 genome.
  • 26/Sep/2017 Fix to bug fix - Bug fix from 80/Sep/2016 (below) didn't get into effect. Now in effect.
  • 26/Sep/2016 Minor bug fix - The sam heading for the after-blat filter files said "SO:coordinate" instead of the correct "SO:unsorted". Now fixed.
  • 26/Sep/2016 Bug fix - The sam-->bam transform in the end of pipe made zero-size files for the convenience files "CAPTURE" and "ALL READS" (combined files for all capture sites) - see above. Now fixed.
  • 26/Sep/2016 Bug fix - The sam-->bam transform in the end of pipe just renamed the file as bam, but the file was actually still sam. Now fixed.
  • 08/Sep/2017 Bug fix - Misunderstanding of the blat parameters used to filter out duplicate regions. minIdentity was set to 0, which is way too low - now risen back to 70 (like it was in CC2 and CC3). 
    CC4 blat defaults now : blat -oneOff=0 -minScore=10 -maxIntron=4000 -tileSize=11 -stepSize=5  -minIdentity=70  -repMatch=999999
  • 05/Apr/2016 Improved feature - Changed BLAT filtering defaults, to make BLAT run match current capSequm (on the parts which are applicable here).
  • 27/Jun/2016 Added feature - Added support to hg38 genome. NOTE that ploidy filtering is not conducted for hg38 ! (duke blacklisted not available for hg38)
  • 25/Apr/2016 Bug fix - Typo in BLAT filter reporter log generation caused blat filtering to be skipped (since 05/Apr/2016). Now fixed.
  • 05/Apr/2016 Improved feature - Changed BLAT filtering defaults, to make BLAT run faster. 
    CC4 blat defaults now : blat -oneOff=0 -minScore=20 -maxIntron=4000 -tileSize=11 -stepSize=5  -minIdentity=0  -repMatch=999999
  • 16/Jun/2016 Improved feature - Sloppy restarting (without cleaning run and public folders after run before restart) causing wonky analysis and broken hubs is now officially PROHIBITED and will result in run crash.
  • 04/Apr/2016 Added feature - Added no-crash behavior to avoid crashing runs when the pipeline is updated
  • 01/Apr/2016 Added feature - Added BLAT filtering custom flags --stepSize --tileSize --minScore --maxIntron --oneOff
  • 01/Apr/2016 Improved feature - Changed BLAT filtering defaults. 
    CC4 blat defaults now : blat -oneOff=1 -minScore=20 -maxIntron=(blat default) -tileSize=11 -stepSize=5  -minIdentity=0  -repMatch=999999
CC3/CC2 old defaults :  blat -oneOff=0 -minScore=30 -maxIntron=4000           -tileSize=11 -stepSize=11 -minIdentity=70 -repMatch=(blat default)
  • 31/Mar/2016 Clarification - Output folder names changed to be more descriptive.
  • 31/Mar/2016 Added feature - Added summary figure of the whole analysis to the statistics page.
  • 24/Mar/2016 Bug fix - Typo in the hub generation broke the combined output hub. Now fixed.