yarden/rnaseqlib

Create initialization module

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yarden commented

Initialization module should:

  • Automatically build the indices (with chrRibo, chrMito) if not already present

    • Download ribo/mito sequences if not present....

  • Download relevant UCSC tables, potentially converting to GTF/GFF if necessary (for Tophat)

  • Check that Tophat/Bowtie/etc. is present

  • Fetch the relevant genomic coordinates (as bed) for:

    • intergenic
    • exonic
    • cds
    • UTR regions...

    so that these maybe used for QC/RPKM.