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mhammell-laboratory / TEsmall

A pipeline for profiling TE-derived small RNAs
GNU General Public License v3.0
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How to skip cutadapt #20

Open JGriffin17 opened 2 months ago

JGriffin17 commented 2 months ago

Hello,

I don't have access to the raw FASTQ files - I only have Trimmed reads. Is there anyway of skipping the cutadapt part of the pipeline and going straight to bowtie to remove the rRNA?

Thanks!

olivertam commented 2 months ago

Hi,

Assuming that the trimming was done correctly, cutadapt should not do much to the trimmed read. You can always check how much additional trimming was done in the log files, but it should have minimal impact (just time spent).

Thanks.