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Old 02-24-2015, 12:27 AM   #1
Location: Portugal

Join Date: Nov 2010
Posts: 11
Default Casava FASTQ from SRA

Dear all,

I am currently trying to perform quality checks on a set of FASTQ files (downloaded from SRA) that (according to the authors) were generated using CASAVA 1.8.1 pipeline.

Since all files belong to a single sample, I am trying to use "--casava" option in FASTQC but I keep getting the "SRR*.fastq.gz didn't look like part of a CASAVA group" error.

To my understanding, FASTQC requires that all CASAVA generated files should be named <sample name>_<barcode sequence>_L<lane>_R<read number>.<0-padded 3-digitset number>.fastq.gz

However, the fastq files from SRA have a very different name: "SRR*_1/_2.fastq.gz"

Is there a way to change the name of these files so that FASTQC recognises them as a single sample or should I just analyse them independently?

Thank you very much in advance,
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