As I am using SNPiR (A pipeline for the detection of SNPs in RNA seq data) for identification of RNA-seq variants.
So during the step of filtering varients, I am using perl script to remove mismatches at 5' read ends with input of raw variants. My input raw_variants.txt file contains 46597831 total no of lines.
So the problem is this script is taking too long even after running for 5 days on 12 cores , it did't got finished.
It would be really helpful to know any alternative way to this step ?
Any help! Thanks a lot.