Here are my quality plots:
I think the forward reads look ok. I was planning on truncating it based off of a quality score of 20. The reverse aren't so impressive. I'm not sure why (maybe because the sample was a lower biomass?). Is there anything wrong with just tossing the reverse reads and redoing demux without them? Or is it better to keep them?
There’s nothing wrong with ignoring the reverse reads, sometimes you have bad luck. Your forward reads still represent your observation of your target region, you just don’t have the length you were hoping for.
You actually do not need to redo the demux step, you should be able to pass your paired-end reads to most single-end methods, they will just only use the forward reads and ignore the reverse.
Hope that helps!
Thank you! This did help!
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