From: Ole K. T. <o.k...@bi...> - 2012-09-06 19:09:08
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Hi, I just ran merTrim on a relatively low coverage library, well, we don't really know whether it is low coverage or not since we don't know the genome size accurately yet. The original library was 16 Gbp, but after merTrim and then loading it into an assembly, only 6 Gbp survived. This might give a relatively good assembly, but I'm a bit worried that it removed too much sequence. Can I adjust how much it throws out? My reads are 150 bp, PE. I followed the preprocessing page on the CA site, and created a database of trusted kmers and used that to correct my reads. Of 56,188,107 reads of mate 1, 18,030,094 were deleted and 36,122,767 were clean, and the average length dropped to 68 bp. I expected it to remove about 10 % of my sequences (from what I've seen on other merTrim runs), but 2/3 seems a bit much. Thank you. Ole |