I was having a different computational problem, I had to compare a single end RNA-seq to paired end RNA seq. So my approach was to take the forward strand reads from the paired end sample and trim the read length and quality score of this fastq file and then map it using BWA, followed by regular stuff of estimating RPKM.
But how can I trim the read length and quality score?
any one liners in perl or awk to do this or is their something in picard tools?
Please share your experience and knowledge.