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  • what is cutoff value in removing short, adapter-trimmed illumina's small RNA reads?

    Dear everybody,

    I have done small RNA sequencing using MiSeq. The raw read length is 51 bp Single End. then I trimmed the adapter using cutadapt. I read in other journals that the next step is to remove reads shorter than certain length, because it might affect downstream analysis. I want to do this but got confused because 2 papers remove reads less than 18 nt (i quote the reason "because such short sequences cannot be traced to genomic loci with high confidence", while other papers remove reads less than 15 nt (no explanation).

    so my question is:

    Which cutoff value should i choose in removing short reads after adapter trimming, on small RNA analysis? and what is the consideration on choosing the cutoff value for removing short reads in smallRNA analysis?

    I hope my English is comprehensible.

    Thank you very much before.

  • #2
    I've been told by someone who studies uRNA here that they don't exist below 17bp, which is why we set our cutoff there. I don't know if that's true or not, though. Anyway:

    because such short sequences cannot be traced to genomic loci with high confidence
    That's kind of silly; the same can be said of 18bp sequences. There's no threshold at which things suddenly become high-confidence; genomes contain repeats of many different lengths.

    Comment


    • #3
      Thank you Brian Bushnell for the input and the opinion

      Comment

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