Cutdapt for batch processing ?

I had around 100 fastq files to be preprocessed wish to use cutadapt for removing adapters. How I do as a batch in one go. Suggestions please.

genome rna-seq sequencing

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updated 6.5 years ago by Asaf

• written 6.5 years ago by sunnykevin97

what did you try ? start maybe by a combination of ls and xargs ?

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written 6.5 years ago by Nicolas Rosewick

Please search biostars in future (use google search since the built in search does not work that well):
cutadapt loop and paired-end reads
C: Bash Script Loop Help

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written 6.5 years ago by GenoMax

1 answer

Use pipeline management system like nextflow, snakemake or wdl/cromwell.

And make sure you have to actually use cutadapt. If your next step is mapping to the genome you're probably good without removing adapters.

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written 6.5 years ago by Asaf

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