Workflow from base calling to pychopper?

nanoporetech / pychopper

A tool to identify, orient, trim and rescue full length cDNA reads

Other

80 stars 22 forks source link

Workflow from base calling to pychopper? #4

Closed cgjosephlee closed 5 years ago

cgjosephlee commented 5 years ago

I have base called using albacore and the primer/adaptor/barcode are removed after base calling. So if I want to run the pychopper and pinfish pipeline, should I base called with keeping all the primer/adaptor/barcode sequences? and remove the primer/adaptor/barcode after running pychopper?

ps. I don't see a variable in albacore is to keep the primer/adaptor/barcode, would you suggest using another base caller?

bsipos commented 5 years ago

Hello,

Albacore will only perform barcode demultiplexing if the --barcoding option is specified. Whatever options you are using, albacore will not remove the reverse transcription primers. Pychopper is looking for those, hence you can use it after basecalling with albacore,

Regards, Botond