What to do with unpaired reads post-trimming?
After Trimmomatic, I am left with a large number of unpaired (orphaned) reads. Are they ultimately useful?
I could include them for assembly with megahit. But a few downstream tools don't deal well with mapping and/or counting orphaned reads, notably htseq. So, does it make sense to assemble including orphaned reads but then ignore them in everything that follows?
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willnotburn •
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