How can I get polyA position and coverage from polyA(+)RNASeq data?

Question

[Ri]

Hi everyone!

As polyA(+) RNAseq library produce reads with polyA tails, is there any way I can extract the position and coverage informations of reads that contain polyA from mapped sam/bam file?

Thank you!

Answer 1

[benformatics]

Just grep the FASTQ for 'AAAAAAA$' and pull the read names. There is no way that the reads aligned without soft-clipping anyway.