Hi all,
I want to discard the reads that overlap some blacklist regions, so I use
intersectbed -abam -v -a readfile.bam -b badregions.bed
I get 9 entries in BED format, despite the abam option ("The A input file is in BAM format. Output will be BAM as well.")
Now if I add the -wa option I get 3.5M entries, again in BED format.
Any idea about what is going on?
thanks
I want to discard the reads that overlap some blacklist regions, so I use
intersectbed -abam -v -a readfile.bam -b badregions.bed
I get 9 entries in BED format, despite the abam option ("The A input file is in BAM format. Output will be BAM as well.")
Now if I add the -wa option I get 3.5M entries, again in BED format.
Any idea about what is going on?
thanks
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