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novoalab / EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
GNU General Public License v2.0
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polyA tails mapping #96

Closed Cynthia0411 closed 3 years ago

Cynthia0411 commented 3 years ago

When I tried to remap the data from SRP174366, I found that they are all perfectly mapped to the reference. However, based on the in vitro transcription process, there should be a polyA tail followed the "curlcake sequences". And as your trimming process is only 5 in 5' terminal and 3 in the 3' terminal, I was wondering where the polyA tails gone. Thank you very much.

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Huanle commented 3 years ago

Hi @Cynthia0411 ,

PolyA tail sequences can not be basecalled at least for now. The ends-trimming was originally (for version1.0) done to remove low-qualities bases at ends. You can skip it now as it does not significantly affect mapping. Hope this helps. Let me know if you have any doubts.