Nanopore: Should you remove reads below certain length ?
We are using Nanopore for some transcriptomics analysis and I am building a QC pipeline. There is a default statement that it could be good to remove reads below 500 bp in length but I could not find arguments for or against this in the literature.
So my question is, assuming that the quality of the read is good, is there an argument why one should remove shorter reads below a certain threshold ( except of course like super short stuff like 10 or so) ?
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