Hi all, I would like to know how genomeCoverageBed deals with secondary alignments in a sam/bam file. I have a set of sam files generated with bowtie2 using the -a flag and I would like to generate a coverage map with genomeCoverageBed. These are the steps that I normally do to obtain a bam file to use for coverage estimation:
1 - Mapping reads with bowtie2 2 - Converting sam to bam and sorting output with samtools 3 - Removing duplicated reads with Picard (MarkDuplicates) 4 - Sorting output again with samtools 5 - Generating a coverage map with genomeCoverageBed
Actually, I tried to map my reads both with and without the -a flag and I got slightly different results. Is it possible that bedtools included secondary alignments in the coverage map? If this is not the case, how does genomeCoverageBed deal with secondary alignments?
Thanks in advance,