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nanoporetech / pychopper

A tool to identify, orient, trim and rescue full length cDNA reads
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WARNING: No reverse complement for U found, returning argument #34

Closed yazuo0204 closed 4 years ago

yazuo0204 commented 4 years ago

Hi,

I used a direct RNA sequence which filtered by NanoFilt for test, but it gave me millions of warnings. image Then when I looked in to the full_length.pdf, it presents that most of the reads is unusable. This raw data looks fine in other Software test, do I need to modify it before running pychopper? image

Thank you !

bsipos commented 4 years ago

There is no reason to use pychopper on direct RNA reads as they do not have the primers attached by chemistry. Hence pychopper is not prepared to take RNA sequences containing Us.