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History / ngs_TRIM

Revisions

  • Major change to TRIM with new behavior. * Added -p flag to turn on padding of paired-end reads with N’s, such that reads are same length. This was the default for paired-end reads. THIS IS NO LONGER ON BY DEFAULT as this has potential adverse affects with the STAR aligner. * Set -m default to 0 and regain original functionality with change to PIPELINE.

    @safisher safisher committed Aug 5, 2014
    7c0a03d

  • Major changes to TRIM. * Added quality score thresholding. * changed behavior of -c: users can run TRIM without a contaminants file. Pre-existing behavior encoded in PIPELINE. * changed behavior of -kN (replaced with -rN): now the default is to not remove N’s from end. Use -rN to remove N’s which is consistent with trimReads.py. The -rN flag has been added to PIPELINE. * changed behavior of -rAT: now default is not removing poly-A/T. Pre-existing behavior (trim 26 bases) now coded in PIPELINE.

    @safisher safisher committed Aug 5, 2014
    4333a08

  • minor tweak.

    @safisher safisher committed Mar 18, 2014
    2de715f

  • moved repo description to own page, documented globals Documented the global variables that are hardcoded in ngs.sh Moved the repository description from Home to DataRepo.

    @safisher safisher committed Aug 23, 2013
    c5c321b

  • tweak

    @safisher safisher committed Aug 22, 2013
    d458196

  • updated todo. fixed TRIM docs.

    @safisher safisher committed Aug 22, 2013
    0d38699

  • tweaks

    @safisher safisher committed Aug 22, 2013
    c9a47d2

  • expanded TRIM

    @safisher safisher committed Aug 22, 2013
    2370a62

  • tweaks

    @safisher safisher committed Aug 22, 2013
    71fced6

  • added TRIM

    @safisher safisher committed Aug 22, 2013
    e6a80c0