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  • Script for counting transcripts in RNA-Seq datasets with random n-mers in the adapter

    This will only serve a small niche of people doing RNA-seq, but figured I'd post it here anyway.

    I wrote a script that essentially implements the counting described here:



    If you have an n-mer of random nucleotides at the end of your RNA-seq adapter, you can use that n-mer to count the number of molecules of RNA. Basically, if you have.

    This script takes a FASTQ file and collapses it based on the barcode. For example, if you have the reads

    GAGAGAGAGGGGGGGGGG
    GAGAGAGAGGGGGGGGGG
    CACACACAGGGGGGGGGG

    and the barcode is the first 8 nucleotides, it gets collapsed down to

    GGGGGGGGGG
    GGGGGGGGGG

    since it is likely that the first two barcodes arose from PCRing the same molecule.

    GitHub is where people build software. More than 100 million people use GitHub to discover, fork, and contribute to over 420 million projects.


    Requires: Python 2.7, numpy, and biopython.

    Best,
    David

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