Question: Not-Merged Reads What to do?
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gravatar for las996
12 months ago by
las9960
las9960 wrote:

Hey guys, So I'm working with pair-end data and I'm concerning regarding the merged/not-merged reads. I'm currently merging them using PEAR and QIIME 2, but I would not like to discard those not merged reads. Should I treat them as "single-end"-like reads? Or it is best to discard them? I'm worried I'll loose too much information if I simply discard not-merged reads. Thank you.

assembly • 233 views
ADD COMMENTlink modified 12 months ago by gb1.8k • written 12 months ago by las9960

What do you aim to do with those reads?

ADD REPLYlink written 12 months ago by WouterDeCoster44k

Align them against reference genome, with Diamond, and then build contigs with the reads, using SPAdes. I'm not sure if it works to treat them all as single end

ADD REPLYlink written 12 months ago by las9960

Do you expect it to merge? I dont think merging is needed if you do an assembly: Should I merge forward and reverse reads before mapping

ADD REPLYlink written 12 months ago by gb1.8k

Hello las996!

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=89795

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 12 months ago by Pierre Lindenbaum129k
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