alignment summary from tophat

Question

[hana]

Hi

I would like to know how can I get the summary of alignment form tophat output. I have looked at the alignment_summary.txt generated by tophat, but I want to know how many reads aligned to two or five locations in the genome and how many aligned to six or more location?

Thanks in advance

Answer 1

[roy.granit]

Not sure there is an 'easy way' to do this. You have to parse the accepted_hit.bam (you can view it using samtools) and count the number of repeating mappings (see http://samtools.github.io/hts-specs/SAMv1.pdf to understand the format.)

Answer 2

[madk00k]

Try using QualiMap to analyze the resulting alignment. There are 2 modes possible: RNA-seq QC or BAM QC with GTF file.