PureCN removemapq0 parameter
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twtoal • 0
@twtoal-15473
Last seen 6 months ago

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 • 306 views
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@markusriester-9875
Last seen 28 days ago

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. 

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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. 

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