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rr1859 / R.4Cker

MIT License
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Ignore QC filter #32

Open rantingswede373 opened 7 years ago

rantingswede373 commented 7 years ago

Hi,

I was wondering if there was a way to ignore the coverage filter for the QC step. I'm getting an odd error that reports <40% coverage near the bait for some (not all) of my samples. I get that this may be important for downstream steps, however the coverage is >40% in all cases as reported by the package and confirmed with analysis using other pipelines.

alb_M2.bg has < than 40% ( 57.4001726427419 %) coverage near the bait. Does not pass QC. alb_F1.bg has < than 40% ( 55.773739228662 %) coverage near the bait. Does not pass QC. alb_F2.bg has < than 40% ( 57.0988018382565 %) coverage near the bait. Does not pass QC. alb_F3.bg has < than 40% ( 46.5026545678106 %) coverage near the bait. Does not pass QC. alb_F4.bg has < than 40% ( 48.7524785710004 %) coverage near the bait. Does not pass QC.

rr1859 commented 7 years ago

Hi,

Thanks for pointing this out. It was checking for perc of sites near the bait but outputting the perc reads in cis. Please update and try again now.

perlp commented 6 years ago

I got the following information, could you please let me know how to solve it? Can i ignore this? Many thanks!

~/4Cker/R1_mapped_modified.bedGraph has < than 40% ( 39.1326530612245 %) coverage near the bait. Does not pass QC.