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epi2me-labs / pychopper

cDNA read preprocessing
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How to combine pychopper with other adapters-removing tool? #25

Closed qiuyixmm closed 1 year ago

qiuyixmm commented 1 year ago

Hello, I want to obtain oriented and trimmed full-length Nanopore cDNA reads without adapter sequences. Porechop is a tool for finding and removing adapters, which I want to use for my Nanopore cDNA reads. I am not sure which tools (pychopper or porechop) I should use first to process my Nanopore cDNA reads. Would you like to give me some advice? BTW, is it necessary to remove adapter sequences when raw Nanopore cDNA reads are processed by pychopper? Thanks!

nrhorner commented 1 year ago

Hi @qiuyixmm

Pychopper will generate adapter-trimmed reads for you; there should be no need to run Porechop as well.

Please try it out and post another message if you encounter any problems.