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nanoporetech / pychopper

A tool to identify, orient, trim and rescue full length cDNA reads
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Using pychopper with DCS108 data #57

Open alexey-larionov opened 3 years ago

alexey-larionov commented 3 years ago

I run the pychopper with DCS108 data. I use DCS primers as provided by Nanopore:

VNP ACTTGCCTGTCGCTCTATCTTCTTTTTTTTT SSP TTTCTGTTGGTGCTGATATTGCTGCCATTACGGCCGGG

Th sequences are taken from https://community.nanoporetech.com/attachments/1459/download

I follow your example for custom primers usage:

cdna_classifier.py -m edlib -b custom_pimers.fas -c primer_config.txt input.fq full_length_output.fq

However, the pychopper output still includes line saying "Using kit: PCS109"

Why I still have this line ? May I be sure that the correct DCS108 primers have been actually used ?

nextgenusfs commented 3 years ago

I think the primers are the same between the kits, so it should be okay.