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epi2me-labs / pychopper

cDNA read preprocessing
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Trim adapter #60

Closed lalalagartija closed 5 months ago

lalalagartija commented 6 months ago

Hi,

pychopper seems very effective to identify adapters but is unable to remove them on the contrary of what is said here : https://github.com/epi2me-labs/pychopper/issues/25

Here is the line I used : pychopper -m edlib -b $adapter -r pychopper_report_${outname}.pdf -S pychopper_report_${outname}.stats -t $THREADS -u ${outname}_pychopper.fastq $reads ${outname}_classified_pychopper.fastq

Is there any way to remove adapters or at least know the positions where they were found ?

Thank you in advance,

nrhorner commented 6 months ago

Hi @lalalagartija

Adapters should be trimmed if the correct kit is specified. What kit are you using?

nrhorner commented 5 months ago

Closing due to lack of response