How do I trim my FASTQ pairs to be at least 50 bp?
How do I trim my FASTQ pairs to be at least 50 bp?
- Some core facilities or commercial sequencing companies only run higher cycle kits (e.g., 2 x 150, 2 x 200). We only require 2 x 50. If you need to trim your reads, follow this procedure:
- Use the following commands to trim your reads using chopper:
conda install -c bioconda chopper
gunzip -c file_R1.fastq.gz | chopper --tailcrop 10 | gzip > file_cropped_R1.fastq.gz
Here, --tailcrop 10 chops 10 bases from the end of the reads. So for 150 bp, it should be --tailcrop 100.
Reference document: https://github.com/wdecoster/chopper