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How to apply CUTADAPT on multiple fastq files using linux?

Hi all,

I'm using CUTADAPT to edit fastq files (from Illumina bulk RNA-seq) before alignment with two targets:

  1. removing adapters
  2. removing poly-A

I'm using terminal on a mac to execute the commands. I've managed to do it as an example on a single fastq but would like to do it on multiple fastq files. I understand it is more of a LINUX question but hopefully would manage to get some help.

All the best.

cutadapt rna-seq r linux conda
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by MatStat MatStat

2 answers

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written by Pierre Lindenbaum Pierre Lindenbaum
  1. get a list of files (look for what find command do)
  2. iterate over the same command (look for for or parallel)
  3. take a coffee meanwhile this is running
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written by JC JC

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