Question: PureCN removemapq0 parameter
0
gravatar for twtoal
14 months ago by
twtoal0
twtoal0 wrote:

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?

 

purecn removemapq0 • 234 views
ADD COMMENTlink modified 14 months ago by markus.riester110 • written 14 months ago by twtoal0
Answer: PureCN removemapq0 parameter
0
gravatar for markus.riester
14 months ago by
markus.riester110 wrote:

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. 

ADD COMMENTlink written 14 months ago by markus.riester110

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. 

ADD REPLYlink written 14 months ago by markus.riester110
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