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Old 12-15-2016, 04:48 PM   #102
j.m.c
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Location: Vancouver BC

Join Date: Dec 2016
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Thank you for your reply.

Yes, my reads were 87 bp after trimming with trimmomatic. I had also removed adapter sequences with trimmomatic and now I think I see the issue if understood correctly what you said:

"The 35bp reads you ended up with are because of the short insert. When you have 2x87bp reads with a 35bp insert, you get 35bp of overlap on the 3' end and then 52bp of the 5' end overhanging on each side; that's adapter sequence. BBMerge trims that off so you are left with only the 35bp of genomic sequence. "

That means the overhangs are removed since BBmerge thinks they are adapter sequences. My reads are from RNA-seq data (not genomic data, I am sorry I didn't specify earlier) and since I removed adapter sequences with trimmomatic, I am actually loosing data if the 5' overhangs were trimmed off...

Is there any way to prevent that with BBmerge?

Otherwise I will try BBmerge with my raw reads without removing adapters.

Thanks!
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