Do you have any guidance on trimming FASTQ files to 2 x 50?

Some cores or commercial sequencing companies only run bigger cycle kits (2 x 150, 2 x 200, etc.). We only require 2 x 50. If you need to trim your reads, this is how you do it.

General guidance for read length for informatics is as follows:

a. MINIMUM of 50bp for both READ1 and READ2

b. All READ1 must be the same length

c. No adaptor trimming has been performed on READ1

d. READ2 can be variable length

To trim your reads:

Tailcrop (end of read) cropping:

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