View Single Post
Old 04-17-2017, 12:37 PM   #459
Brian Bushnell
Super Moderator
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Hi Kristian,

Is this a Nextera long-mate pair library? Those need special processing before they can be mapped. Or... can you give me any more information about the library construction, and the trimming methodology? The library has an extremely high error rate (particularly with read 2), less than half of the reads map to the mito, and it appears that both adapters and transposase are still present.... also, I'm measuring the median insert size as 159 (BBMap) or 133 (BBMerge), so there are a lot of pairs with insert size shorter than the sequenced read length; those might be displayed differently in IGV depending on whether the adapter portion was soft-clipped (which bwa would do by default) or not (bbmap does not soft-clip by default).

I adapter-trimmed the reads and error-corrected them, but still under 50% map. I'm not really sure what's wrong with the library. But, I don't see anything unusual about the pairing orientations. I get 45.5670% properly paired with "rcs=f" (require correct strand = false) and 45.5481% with "rcs=t", so only 0.02% map in the wrong orientation.

Last edited by Brian Bushnell; 04-17-2017 at 03:38 PM.
Brian Bushnell is offline   Reply With Quote