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rrwick / Porechop

adapter trimmer for Oxford Nanopore reads
GNU General Public License v3.0
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After back-transcription, can porechop be used for direct RNA seq kit data? #30

Closed phiweger closed 6 years ago

phiweger commented 6 years ago

Or might it even work on the raw data?

Thank you, Adrian

rrwick commented 6 years ago

Hi Adrian,

It certainly won't work on the raw data yet, as I haven't included RNA adapter sequences in Porechop.

Does back-transcription mean converting the reads to a complementary DNA sequence in silico? If so, Porechop might work, but only if direct RNA uses the same adapter sequences as other kits. If not, the adapters will need to be added to the adapters.py file. I can be challenging to actually get the adapter sequences - Nanopore doesn't always publish them (or publish them in their entirety).

Ryan

rrwick commented 6 years ago

Closing now because direct RNA reads are discussed in issues #27 and #40.