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Old 05-07-2013, 09:34 AM   #1
jgibbons1
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Default fastq.gz stats READ-COUNT BASE-COUNT

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

Last edited by jgibbons1; 05-07-2013 at 09:35 AM. Reason: forgot to mention something
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Old 05-07-2013, 10:12 AM   #2
GenoMax
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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.
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Old 05-07-2013, 10:21 AM   #3
maasha
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Biopieces (www.biopieces.org) have a bunch of useful tools:

https://code.google.com/p/biopieces/...aning_NGS_data
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Old 05-07-2013, 10:21 AM   #4
jgibbons1
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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!
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Old 05-07-2013, 10:27 AM   #5
jgibbons1
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Ahhh...biopieces...hadn't thought about that.

Thanks
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Old 05-07-2013, 10:30 AM   #6
jgibbons1
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Unfortunately, I don't think Biopieces takes compressed fastq files as an input option (with the read_fastq option).
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Old 05-07-2013, 10:48 AM   #7
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Biopieces reads gzipped files.
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Old 05-08-2013, 06:40 AM   #8
WaltL
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Quote:
Originally Posted by GenoMax View Post
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.
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Old 05-08-2013, 07:08 AM   #9
maasha
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Of cause Biopieces can do that. Check this out:

https://code.google.com/p/biopieces/...nce_statistics
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Old 10-30-2013, 05:24 AM   #10
atrx
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Quote:
Originally Posted by maasha View Post
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.
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