I used the option --removemapq0 when I ran Coverage.R, since it seemed reasonable that reads with 0 mapping quality should be removed. There isn't any non-obvious reason why this is a bad idea, is there?
You'll probably get a significant drop in off-target coverage with removemapq0. There is information in those reads and on-target regions with poor mapping are ignored anyways.
I would recommend following the vignette closely and using the defaults for test runs and then work from there.
I checked a few datasets and it appears to be safe to remove those reads. I didn't see a huge impact. Let me know if it improves your results.
Login before adding your answer.
Use of this site constitutes acceptance of our User Agreement and Privacy