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.
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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