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Old 12-28-2015, 06:17 AM   #6
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Location: Germany

Join Date: Oct 2008
Posts: 415

I analysed some public MNase data recently for a large complex genome >2gb and had this issue too with 50bp reads. There appears to be a very high background in MNase data.

Longer read lengths might partially mitigate the issue. However, if MNase indicates you are primarily sequencing complex repeats this problem will always occur if read lengths are shorter than the compound repeats. Interestingly, those using the data are very happy with it, especially the patterns around gene boundaries appear as expected.

To practically deal with it I have produced two tracks, one with all reads and one filtered by samtools to only include Mapping Quality 20+ reads.
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