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epi2me-labs / pychopper

cDNA read preprocessing
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trim out PCS111 UMI #49

Closed camillaugolini-iit closed 9 months ago

camillaugolini-iit commented 10 months ago

Hi,

I would like to know if there is an option not only to detect the UMI from kit PCS111 and add them to the BAM tag, but if I can remove them directly from the fastq before the mapping.

Thanks a lot

Camilla

nrhorner commented 10 months ago

Hi @camillaugolini-iit

The workflow does not currently trim adapters barcodes and UMIs from reads but is something we are considering adding soon.

edit: I was think about a different workflow there, sorry Thanks,

Neil

nrhorner commented 10 months ago

Hi @camillaugolini-iit

In my previous message I was on the repo for a different workflow, sorry for any confusion caused. It's not currently possible to remove the UMI from the read with Pychopper currently. We will consider adding that functionality

nrhorner commented 9 months ago

Closing due to lack of response