What config.txt should I use for a direct cDNA kit ?

[alexey-larionov]

Lines 275-276 in
https://github.com/nanoporetech/pychopper/blob/master/scripts/cdna_classifier.py
say:

if args.x == "DCS109":
CONFIG = "-:VNP,-VNP"

What is the meaning of this config?
What config.txt should I use for a direct cDNA kit ?

Thank you for the great tool :)

[callumparr]

config tells pychopper in what orientiation to expect your adapter/primer sequences used to make the full-length cDNA library. So for instance it be odd to have a read that both start and finished with a SSP sequence or VNP sequence. Depending on whether the sequence is the original mRNA or cDNA copy you expect a certain orientation. For cDNA kit from nanopore you should not need to change anything other you can invoke a specific flag in a second pass to rescue chimeric reads generating during the cDNA library prep I think. Did you read the README?