Number of Reads

[hamcan]

Hi there,
I have Illumina HiSeq fastq output files. I want to know how I can find out the number of reads per sample before and after processing using unix.
Any commands that you might know of?
I'd greatly appreciate it
Thanks!

[mastal]

 wc -l

gives you the number of lines. Divide that by 4 to get the number of reads.

[wdecoster]

If the file is not compressed:

grep -c '^@' yourfile.fastq

If the file is gz compressed:

zcat yourfile.fastq.gz | grep -c '^@'

If the file is depressed:

talk to it about feelings and give chocolate

[jdk787]

You can also run it through FastQC before and after processing. This will give you number of reads and a lot of other useful information.

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

[mastal]

The quality scores may sometimes have a value '@', so you may have some of the base quality lines also beginning with '@'.

[wdecoster]

The quality scores may sometimes have a value '@', so you may have some of the base quality lines also beginning with '@'.

Right, good catch

[LacquerHead]

samtools flagstat

[hamcan]

thanks everyone!
how about to find the number of bases?

[Michael.Ante]

It should be something like

awk 'NR%4==2{print}' in.fastq | wc

With the awk command, you print the nucleotides, with wc you count the output's characters.

[Brian Bushnell]

I like to use BBMap's Reformat:

reformat.sh in=100x.fq

No output stream specified.  To write to stdout, please specify 'out=stdout.fq' or similar.
Input is being processed as paired
Input:                  	3072634 reads          	463967734 bases
Output:                 	3072634 reads (100.00%) 	463967734 bases (100.00%)

Time:                         	3.317 seconds.
Reads Processed:       3072k 	926.30k reads/sec
Bases Processed:        463m 	139.87m bases/sec

That has the advantage of working on fasta, fastq, or sam; compressed or raw. And various other formats.