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Old 10-28-2013, 05:17 AM   #1
hmortens
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Default FASTQC setting for multiple casava fastq files?

I am using fastqc in my workflow, but am wondering how to get the program to recognize multiple cassava fastq files, as described in the manual.
My command for a single fastq is like:
/fastqc –outdir=/unaligned/project_x/ --casava –noextract –quiet /unaligned/project_x/sample_13176/13176_ATCACG_L003_R1_001.fastq

But when I use only the sample directory for the input parameter, the program does not recognize the sample directory. So, it only runs with a single fastq specified.

Can anyone give me an example of how to run on a directory with multiple fastq files (cassava fastq)?

I wrote to Simon Andrews but have not heard back in several days, and need to get on with it.

Thanks.
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Old 10-28-2013, 06:33 AM   #2
mastal
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Have you tried specifying --casava, but also listing all the files that you want analysed together, rather than just giving the name of the directory?
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Old 10-28-2013, 07:30 AM   #3
hmortens
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Simon Andrews just wrote back to clarify...hoorah!
Simple answer, but the manual is not clear on this point.
fastqc --casava *.fastq.gz

Running it now...
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