Given a set of reads from shRNA sequencing, we count how often each reference shRNA sequence occurs at the expected position in the reads.
Each read should contain a barcode at a specified position. We divide the reads according to those barcodes.
This library is pip-installable, or can be run from the source directory.
The reads should be in a set of fastq-files, that can optionally
be gzip compressed.
The shRNA-library and the barcodes should each be stored in a simple
headerless tsv with the two columns id and sequence.
We do not require library sequences to be unique. If a sequence is not unique we print a warning and ignore all but one of the ids.
For usage see ./rnacount.py -h.