Number of reads in FASTQ file

Parharn · 02-17-2014, 10:17 AM

Hi,
How can I just find out how many reads are there in a fastq file?

Thanks,
Parham

Wallysb01 · 02-17-2014, 10:22 AM

wc -l file.fastq will give you the number of lines, then you can divide that by four.

Or you can just run fastqc.

JackieBadger · 02-17-2014, 10:26 AM

Or

grep xxx -c file.fastq

xxx being some string of characters only found in sequence identifiers

With MiSeq generated fastq an example would be

grep @M00 -c file.fastq

Parharn · 02-17-2014, 10:41 AM

Thanks guys.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
count reads number in collapsed file	lran2008	Bioinformatics	2	07-30-2013 11:34 AM
Splitting a BAM file by every x number of reads, not lines.	carmeyeii	Bioinformatics	10	05-06-2013 12:02 PM
Split Large FASTQ file in small FASTQ files with user defined number of reads Windows	deepbiomed	Bioinformatics	3	04-04-2013 08:14 AM
question about random select certain number of reads from ChIP-seq bed file	yaolij@gmail.com	Bioinformatics	1	09-15-2012 03:13 PM
prep_reads file in Tophat run shows a different number of reads	gen2prot	Bioinformatics	7	03-24-2011 02:50 AM

02-17-2014, 10:17 AM	#1
Parharn Member Location: Sweden Join Date: Jul 2013 Posts: 84	Number of reads in FASTQ file Hi, How can I just find out how many reads are there in a fastq file? Thanks, Parham

02-17-2014, 10:26 AM	#3
JackieBadger Senior Member Location: Halifax, Nova Scotia Join Date: Mar 2009 Posts: 381	Or grep xxx -c file.fastq xxx being some string of characters only found in sequence identifiers With MiSeq generated fastq an example would be grep @M00 -c file.fastq Last edited by JackieBadger; 02-17-2014 at 11:34 AM.

02-17-2014, 10:22 AM	#2
Wallysb01 Senior Member Location: San Francisco, CA Join Date: Feb 2011 Posts: 286	wc -l file.fastq will give you the number of lines, then you can divide that by four. Or you can just run fastqc.

02-17-2014, 10:41 AM	#4
Parharn Member Location: Sweden Join Date: Jul 2013 Posts: 84	Thanks guys.