Different results using bamCoverage with or without samFlagExclude

[VirginieJJ]

Hi,

I'm using bamCoverage to generate Bigwig output. When I use samFlagExclude on full Bam alignment (strand + and -), I have different result than use BamCoverage on only one strand without samFlagExclude. By using an home made script results of reverse strand using the full bam all_strand are coherent with obtained results.

Version of bamCoverage 3.5.1 in conda environment

bamCoverage -bs 1 -p 12 --normalizeUsing CPM --samFlagExclude 96 --samFlagExclude 144 -b all_strand.bam -of bigwig -o "output_reverse.bw"

and

bamCoverage -bs 1 -p 12 --normalizeUsing CPM -b reverse_strand.bam -of bigwig -o "output_reverse.bw"

For example, the two first row are bam infos, the third using bamCoverage only on reverse strand, le 4th is using bamcoverage with samFlagExclude.

Thank you,

Virginie