question about using “intersectBed –v –s” to exclude some reads in the bam file

[tinkering]

Hello,

When I used “intersectBed -abam aligned.bam -b genes.bed -v -s -ubam > aligned.filtered.bam” to filter the reads in the aligned,bam that overlap with the entries in genes.bed, the output file “aligned.filtered.bam” has even much bigger size than the original bam file “aligned.bam”. That is not consistent the functions of removing regions in the bam file with “-v” option.

Has anyone met the similar issue when using "intersectBed -v" bedtools?

Any suggestion?

Thanks.

[kmcarr]

The option "-ubam" directs intersectBed to write the output as uncompressed BAM. Since your input was undoubtedly compressed it's not surprising that the uncompressed output is larger even if it actually contains less data.