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Old 06-06-2014, 11:31 AM   #6
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,696

Originally Posted by jimmybee View Post
Ive been using it over the last couple of weeks and it has been really quick. Im actually using it to run adapter trimming (with small inserts, all of your reads should overlap), so adding in some options for adapter matching would be handy (although I do know that you already have a trimming script in the bbtools suite)

FYI, the latest version of BBMerge by default rejects insert sizes shorter than 35 and does not look for insert sizes shorter than 25, so if you have super-short insert libraries, you might want to reduce those with these flags:
mininsert=12 minoi=12

"mininsert" will reject anything shorter than that value as "too short", while "minoi" (minoverlapinsert) will tell the program to not look for inserts shorter than that. The difference is subtle. Sorry, the default values listed for them in the shellscript are wrong; I will fix that with the next release. Of course for most purposes you don't ever see insert sizes that short but you can in certain experiments involving tiny RNAs.

I have no plans to explicitly add adapter matching to BBMerge, but it sounds like it may be useful to add a mode that trims reads with insert sizes shorter than read length rather than merging them. Also, it would be fairly easy to add overlap-detection to BBDuk for greater adapter-trimming sensitivity. Hmmm, I'll probably do both.


For some reason I can't get COPE to work:

/dev/shm$ ./cope -a /dev/shm/sr1.fq -b /dev/shm/sr2.fq -o /dev/shm/cmerged.fq -m 0 -s 33
Program start..
Program: COPE (Connecting Overlapped Pair-End reads)
Version: v1.1.3
Author: BGI-ShenZhen
CompileDate: Jun 6 2014 time: 10:30:24
Current time: Fri Jun 6 10:46:56 2014
Command line: ./cope -a /dev/shm/sr1.fq -b /dev/shm/sr2.fq -o /dev/shm/cmerged.fq -m 0 -s 33
Error: input file is empty, please check the set of input file!
Other programs can see the files fine. I moved them to various places and tried both absolute and relative paths. Any ideas?
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