Subsample fastq to the same sequencing depth

Input

1. Fastq read list. You can get it using ls *fastq.gz > input.list

2. Desired sequencing depth. You first need to count the reads and find the minimal reads in your fastq list.

Usage

hpcf_interactive -q priority

module load python/2.7.13

ls *fastq.gz > input.list

run_lsf.py -f se.list -p subsample_fastq --seqtk_sample_number 30000000

code @ github.