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ChIP-seq updates: estimated fragment length and more #450
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* scRNASeq changes Feb 2020 * March updates * Merging activeDev for v4.0.1 release (#444) * Fix sequenza error * Scrnaseq (#437) Scrnaseq: miRNA-seq changes and scRNA-seq changes * Symlink counts matrix if "counts/" exists in users rawdata directory * Dectect if users is starting from a raw counts matrix * Updating pop-up box dialogue after detection of new counts matrix filetype * Find differential expression metadata in "/path/to/rawdata/counts/" * Readability: checking for counts matrix outside conditional statement * Adding "--alignEndsProtrude 10 ConcordantPair --peOverlapNbasesMin 10" to the first and second pass of STAR * Explicitly loading 'python/2.7': default version of python changing to '3.7' Co-authored-by: Mayank Tandon <mtandon09@gmail.com> Co-authored-by: wong-nw <38703762+wong-nw@users.noreply.github.com> Co-authored-by: jlac <justin.lack@nih.gov> Co-authored-by: Skyler Kuhn <kuhnsa2@mymail.vcu.edu> Co-authored-by: Mayank Tandon <mtandon09@gmail.com> Co-authored-by: jlac <justin.lack@nih.gov> Co-authored-by: skchronicles <kuhnsa2@vcu.edu>
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This update includes a number of improvements to the current pipeline:
improved steps handling estimated fragment length (ppqt) to allow corrections when the first ppqt estimated fragment length is not biologically possible
cleaned up some problems with DiffBind so that the script doesn't automatically die when certain plots cannot be created
made jaccard plots pdfs instead of pngs
made some changes to FRiP plotting, more needed to solve all problems
Changed memory requests for BWA rules