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.
Requires: Python 2.7, numpy, and biopython.
Best,
David
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