Available pipeline versions

updated by Jelena - 16:00 08/Oct/2018

Current releases - fixes and issues

Bug fixes and updates (after release)

Current issues - known bugs and development targets !

CM5 - CCseqBasic5-MultiThread ("Currently developed parallel CC5") Not yet portable (intra-WIMM only). Released 08Oct2018. Current development version.

    CCseqBasic5.sh --help      (CM5)

CM5 is like CB5 below - but capable of running input fastqs in parallel.
Also features the new great "rainbow" visualisations : whole experiment is described by 7 tracks total, not 7 tracks per capture site.
Full user manual still under construction.

New features :

  • Fully parallel (uses queue threads).
  • Uses PIPE_fastqPaths.txt parameter file to read in MULTIPLE fastq files (no catenation of lanes pre-pipeline needed).
  • New visualisations (more feasible to big designs ~ dozens or hundreds of capture sites).
  • Better quality control (raw mapped fragments visualisation, more illustrative description.html page).
  • Normalised tracks (to total reporter counts AND only-cis reporter counts) for all capture sites.
  • Blat-filter generation separated to its own run type with --onlyBlat flag : and by demanding blats to be pre-generated when entering actual production run.

    • CB5 - CCseqBasic5 ("Currently developed CC5") Fully portable. Released 20Nov2017. Current development version.

        CCseqBasic5.sh --help      (CB5)

    CB5 is like CS5 below - but getting all new fancy features.

    New features :

  • Bowtie2 support

    • CS5 - CCseqBasic5 ("Stable portable CC5") Fully portable. Released 17Nov2017. Only receiving minor updates and bug fixes.

        CCseqBasic5.sh --help      (CS5)

    CS5 is like CF5 below.

    Introducing "third way to filter non-flashed reads" :
    Because: CB3a is too lenient to duplicates (of non-flashable reads) and CB4a is too strict - CB5 is "in between" (just goldilocks).

    In CS5 all the pipes merge to a single run command :
    User can call the wanted duplicate filtering mode with --CCversion CS3 or --CCversion CS4 or --CCversion CS5

    Duplicate filtering bug fix : fixing a bug (which apparently hasn't really caused any damage however - so this is smaller fix than it seems)

  • In previous versions CC3/4 CB3/4a duplicate filtering was strand-specific. Now reverting back to CC2 style (non-strand-specific).
  • The CC3/4 CB3/4a "wrong" duplicate filtering can be requested with a flag (backwards compatibility).

    • New features :

  • UMI support with --UMI flag (default is non-umi run) : details to set up UMI run : contact Damien Downes.
  • Wobbly end duplicate filter with --wobblyEndBinWidth flag : non-exact-read-ends duplicate filtering.
    • To turn wobbly ends off, set this to 1 ( --wobblyEndBinWidth 1 ) - this is the default.
    If using --UMI , --wobblyEndBinWidth 20 is recommended.

    For example : --wobblyEndBinWidth 20 means : bin of 20 bases for duplicate filter :
    if all fragment coordinates are the same +/- 10 bases, ( and if --UMI is used : UMI is the same), reads are duplicates.

    CF5 - CCseqBasic5 ("Frozen portable CC5") Fully portable. Frozen in development to 16Nov2017. Only receiving bug fixes.

    Introducing "third way to filter non-flashed reads" :
    Because: CB3a is too lenient to duplicates (of non-flashable reads) and CB4a is too strict - CB5 is "in between" (just goldilocks).

    In CF5 all the pipes merge to a single run command :
    User can call the wanted duplicate filtering mode with --CCversion CF3 or --CCversion CF4 or --CCversion CF5 

        CCseqBasic5.sh --help      (CF5)

    "Frozen in time" releases - stable development end points receiving only bug fixes

    Bug fixes and updates (after release)

    Current issues - known bugs and development targets !

    CB4 alpha - CCseqBasic4 ("First portable CC4") Fully portable. Frozen in development to 16Nov2017. Only receiving bug fixes.

        CCseqBasic4.sh --help      (CB4a)

    CB3 alpha - CCseqBasic3 ("First portable CC3") Fully portable. Frozen in development to 16Nov2017. Only receiving bug fixes. 

        CCseqBasic3.sh --help      (CB3a)