What to do with unpaired reads post-trimming?
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3.5 years ago
willnotburn ▴ 40

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?

de-novo trimming htseq mapping metagenomic • 1.1k views
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