Hi there,

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) ?

Thanks!
As always, one needs to know which downstream analysis you have in mind.

It is recommended, yes, but it doesn't make much sense for transcriptomic data. Many transcripts are [well below 500 nt][1] in length, so you tend to lose information. I lately noticed this in `BUSCO`-analyses. My suggestion would be to try length filtering, and compare it to other measures (while watching out for transcriptome completeness). Filtering for quality with [nanofilt][2], and selection of full-length transcripts using something like [pychopper][3] would be more appropriate in my opinion.


  [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7905317/
  [2]: https://github.com/wdecoster/nanofilt
  [3]: https://github.com/nanoporetech/pychopper