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

CC3 release - launched 27/Oct/2015

Bug fixes and updates in CCanalyser3.pl (after release) :

  • 13/Dec/2015 Support fix - The data0 data area moved (and script stopped working). Now fixed - bigwig generation master file points to the new location.

    • 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) .
  • 28/Sep/2016 Added feature - Added support to danRer10 genome.
  • 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 combined "CAPTURE" and "ALL READS" files. 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.
  • 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)
  • 05/May/2016 Added feature - Added no-crash behavior to avoid crashing runs when the pipeline is updated
  • 13/Feb/2016 Added feature Added flash flag --flashBases 10 (when flashing, has to overlap at least this many bases to combine - default 10 bases )
  • 13/Feb/2016 Added feature Added flash flag --flashMismatch 0.25 (when flashing, max this proportion of the overlapped bases are allowed to be MISMATCHES - defaults to one in four allowed to be mismatch, i.e. 0.25 ) sometimes you may want to lower this to 0.1 (one in ten) or 0.125 (one in eight) or so
  • 13/Feb/2016 Added feature Added flag --qmin to allow user to play with trimming quality values. --qmin 20 is default, but sometimes stricter --qmin 30 may be needed.
  • 15/Dec/2015 Bug fix - The rerun option --onlyCCanalyser was removing the "original run output" SAM file instead of using it in the re-run (typo in samtools view commmand). Now fixed.

    • Bug fixes and updates in Pipe1/pipe.sh (after release) :

  • 04/Dec/2015 Improved feature - The pipeline didn't auto-generate SYMBOLIC LINKS to the bigwigs (but copied the bigwigs to public). Now auto-generates folder "PERMANENT_BIGWIGS_do_not_move" to run folder, thus avoiding clogging the /public/ area.
  • 03/Dec/2015 Bug fix - The pipeline didn't auto-generate public folder "sample" for the data - risked overwrite if running multiple samples with same --pf parameter. Now fixed.