Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads

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glopez • 0

@glopez-14203

Last seen 14 months ago

United Kingdom

Hello,

I have noticed a strange behaviour when using Rsubread in a recent bacterial RNASeq dataset. The use of the nTrim parameters lead to a change in the order of the reads provoking that they do not pair properly (check below). I have tested the same parameters using other samples from a different library and different bacteria and I have not been able to reproduce this issue. I also run this same samples on Star using the parameter clip5pNbases and it worked fine.

Does anyone have an idea about why might this be happening?

Thanks

Rsubread • 608 views

ADD COMMENT • link updated 14 months ago by Gordon Smyth 52k • written 14 months ago by glopez • 0

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Have you cmitted part of your question? The question doesn't show any Rsubread code or any check of output. You would need to show the actual code used and more details about output problems to make help possible.

This is just speculation, but is it possble that you are trimming entire reads in some cases?

ADD REPLY • link 14 months ago Gordon Smyth 52k

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