Breaking News: Grepper is joining You.com. Read the official announcement!

count barcodes in undetermined fastq file

Charles-Alexandre Roy answered on June 2, 2023 Popularity 1/10 Helpfulness 8/10

answer count barcodes in undetermined fastq file

count barcodes in undetermined fastq file

Comment

# Basic syntax:
gzip -cd Undetermined_S0_R1_001.fastq.gz | grep '^@' | cut -d: -f10 | sort | uniq -c | sort -k1rn | less
# Where:
#	- gzip -cd writes the decompressed information from the fastq file to stdout
#	- grep '^@' finds all header rows (could also use awk '(FNR%4==1){print $0}')
#	- cut -d: -f10 splits the line on ':' and returns the 10th item (the barcodes)
#	- sort | uniq -c | sort -k1rn sorts the barcodes, counts duplicates, and
#		then sorts them in reverse by their counts to print the most frequent 1st

Popularity 1/10 Helpfulness 8/10 Language shell

Source: slowkow.com

Tags: count fastq file shell

Link to this answer
Share Copy Link

Contributed on Jun 02 2023

Charles-Alexandre Roy

0 Answers Avg Quality 2/10

Continue with Google

By continuing, I agree that I have read and agree to Greppers's Terms of Service and Privacy Policy.

count barcodes in undetermined fastq file

Contents

More Related Answers

count barcodes in undetermined fastq file

Grepper

Documentation

Social

Legal

Contact

Oops, You will need to install Grepper and log-in to perform this action.