fastq.gz stats READ-COUNT BASE-COUNT

[jgibbons1]

Hi all,

Before I try writing some inefficient code, I was wondering if anyone has a script to count read number and total base count (or average read length) from a gzipped fastq file or even better, a batch of gzipped fastq files.

Thanks

[GenoMax]

FastQC should give you the stats you need: http://www.bioinformatics.babraham.a...ojects/fastqc/

You can use FastQC on the command line or via GUI.

[maasha]

Biopieces (www.biopieces.org) have a bunch of useful tools:

https://code.google.com/p/biopieces/wiki/HowTo#Quality_assurance_and_cleaning_NGS_data

[jgibbons1]

I thought about FastQC, but all really want is Number of Reads and base count or average read length...FastQC does a lot more (which is great) at the cost of time.

It may be my best alternative though.

Thanks!

[jgibbons1]

Ahhh...biopieces...hadn't thought about that.

Thanks

[jgibbons1]

Unfortunately, I don't think Biopieces takes compressed fastq files as an input option (with the read_fastq option).

[maasha]

Biopieces reads gzipped files.

[WaltL]

FastQC should give you the stats you need: http://www.bioinformatics.babraham.a...ojects/fastqc/

You can use FastQC on the command line or via GUI.

I use FastQC all the time. Very nice tool; however, unless I'm missing something, it neither gives the mean read length (it does give the size range and a graphical distribution of read length) nor the total number of bases in a file.

I too would like to find a tool or a script that calcs. the average read length and the total # of bases in a fastq file. I also looked at the documentation for Biopieces, but I don't think it does this either.

[maasha]

Of cause Biopieces can do that. Check this out:

https://code.google.com/p/biopieces/wiki/HowTo#Howto_get_some_basic_sequence_statistics

[atrx]

Of cause Biopieces can do that. Check this out:

https://code.google.com/p/biopieces/...nce_statistics

I check out the Biopieces documentation,but i don't see how to count base pairs.