After back-transcription, can porechop be used for direct RNA seq kit data?

[phiweger]

Or might it even work on the raw data?

Thank you,
Adrian

[rrwick]

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]

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