Read Counts by Tim Shaw

Usage readcounts.py [Input File Location] [Output File Location] [Length of 3' Random-mer]

This program was created for the Lykke-Andersen lab at UCSD for the purpose of processing sequencing results so they can used by other downstream scripts.

readCounts takes an input FASTQ file, trims the random-mer from the 3' end, and counts how many copies of each read there are. In order to remove PCR artifacts, it also compares the 3' random-mer. Matching 3' random-mers are considered to be PCR artifacts and don't contribute to the number of unique reads.

Output read without random-mer, total number of reads, number of unique reads