Not-Merged Reads What to do?
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.
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What do you aim to do with those reads?
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
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
Hello las996!
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