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Old 11-13-2018, 04:09 AM   #1
Junior Member
Location: Israel

Join Date: Nov 2017
Posts: 1
Default Very low merging yield with BBMerge vs PEAR

Hey all,
I'm trying to merge my reads (300bp, demultiplexed) using BBMerge and for my samples, sequencing results of the fungal ITS2 region, BBMerge yields much lower merged reads compared to PEAR (~50% vs ~90%, respectively). Most of the unmerged reads by BBMerge are ambiguous. Few questions:
Is there something I can try with BBMerge?
I've read here that PEAR results in a lot of FP, but can it be up to 50% of the sample?
Many of my reads are longer than the actual length of the fragment sequenced (ITS2 region vary in size, 100-500bp), is BBMerge sensitive to post-adapters "garbage" bases?

I'd rather not to trim my reads based on quality \ primers' sequence since it interferes with follow steps of the analysis.

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Old 11-13-2018, 05:26 AM   #2
Location: UK

Join Date: Jan 2011
Posts: 14

FLASh is a good choice to try.

Last edited by Phoenix_ICE; 11-13-2018 at 05:33 AM. Reason: grammar
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