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nanoporetech / pychopper

A tool to identify, orient, trim and rescue full length cDNA reads
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customised primer configuration #35

Closed ozgegizlenci closed 4 years ago

ozgegizlenci commented 4 years ago

Hello,

I was trying to use pychopper for the primers I designed in my cDNA sequencing with single end barcoded primers. I am trying to understand the configuration file and what it indicates since I was not able to see an explanation about it. 'Where the contents of primer_config.txt looks like +:MySSP,-MyVNP|-:MyVNP,-MySSP.' I would assume the + or - indicates the direction of the primers during the nanopore sequencing of each strand.

Could you please elaborate on it? Thank you Ozge

bsipos commented 4 years ago

Hello,

Indeed + and - before the colon indicate the direction of the sequencing of the read. The - in -MyVNP indicates that the end of the sequence contains the reverse complement of "MyVNP". Also, please remember that the custom primer functionality only works with the edlib backend (unless you train profile HMMs).

Botond