I’m experiencing a filtering issue when I’m running bamCoverage. It’s giving me this message “Due to filtering, 55.52154672723388% of the aforementioned alignments will be used 47470185.12564443.”
I’m running bamCoverage with the following arguments: bamCoverage -b path/to/bam --normalizaUsing RPKM --filterRNAstrand reverse -of bedgraph -o output_file_name bamCoverage -b path/to/bam --normalizaUsing RPKM --filterRNAstrand forward -of bigwig -o output_file_name
I started seeing this filtering message when I added the normalization option to my bamCoverage command (before bamCoverage ran without any filtering issues). I tried adding the “--exactScaling” option to my bamCoverage command, but that only decrease the percentage of the aforementioned alignments being used. Does anyone have any idea why this filtering issue is happening or what can I do to fix it?
Thank you for your help!