How to apply CUTADAPT on multiple fastq files using linux?
2
1
Entering edit mode
9 months ago
MatStat ▴ 140

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 • 345 views
ADD COMMENT
2
Entering edit mode
ADD COMMENT
1
Entering edit mode
9 months ago
JC 12k
  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
ADD COMMENT

Login before adding your answer.

Traffic: 1500 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6