Awk Command to Count Total, Unique, and the Most Abundant Read in a FASTQ file
Year: 2012
Type: other
Abstract: I was reading through a paper on comparative ChIP-Seq when I found this awk gem that lets you get some very basic stats very quickly on next generation sequencing reads. To use, simply cat the fastq file (or gunzip -c) and pipe that to this awk command: cat myfile.fq | awk '((NR-2)%4==0){read=$1;total++;count[read]++}END{for(read in count){if(!max||count[read]>max)
DOI: 10.59350/7x4jr-ws733
Author: Stephen Turner
Institution: University of Virginia
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
OpenAlex ID: W4417085360