How to apply CUTADAPT on multiple fastq files using linux?

Question

[MatStat]

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.

Answer 1

[Pierre Lindenbaum]

• use a loop. https://www.cyberciti.biz/faq/bash-for-loop/
• use a Makefile e.g: Is it possible to run variant calling software in parallel, are there any Shell and Python/R code examples available?
• use a workflow manager : snakemake, nextflow etc...

Answer 2

[JC]

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