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nanoporetech / pychopper

A tool to identify, orient, trim and rescue full length cDNA reads
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How to choose reads type to the downstream process? #30

Closed huangziyan11111 closed 4 years ago

huangziyan11111 commented 4 years ago

Hi, I am processing the nanopore data for transcriptome analysis, I want to know that I need just use the reads_full_length.fq or I can use all the output reads (reads_full_length.fq + rescued.fq + unclassified.fq) to downstream analysis? If I can use all the reads, the purpose of "cdna_classifier.py" is to trim the primer sequence, is that right?

bsipos commented 4 years ago

You only need the reads_full_length.fq.

huangziyan11111 commented 4 years ago

@bsipos Could you tell me why unclassified.fq can't be used？

bsipos commented 4 years ago

Because they do not have one or both PCR primers identified. Hence they are not guaranteed to be full length in sequencing and their orientation cannot be determined.