Question: fastq files are't recognized by tools
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markus.wolfien • 50 wrote:
Hey,
I'm looking forward to do some NGS analysis and would like to use your provided NGS tools. I uploaded some of my .fastq files (standardized in illumina 1.9) as fastq format. But somehow the tools, e.g. FASTQGroomer, don't recognize the data not as FASTQ. Is this a problem of data preprocessing, uploading or something else? I also tried to upload the files as illuminafastq but the errors are still the same.
Thanks for your efforts and best regards,
mwolfien
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modified 4.0 years ago
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dtabed • 0
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4.6 years ago by
markus.wolfien • 50
Thanks a lot. I changed the datatype and now everything is fine.
Great! Since this worked for you, please mark the answer below as accepted. This allows us to more easily find and help people with questions that remain open.
Hey again,
now it recognizes the data, but during the uplaod (upload as fastqsanger) the fastq file is a kind of malformed. The upload somehow changes the first line of the file and adds the name of the file in front of the first @. Therefore the tools generate an error. May changing the upload procedure will help, because I currently upload the data directly from .tar.gz files and not from a ftp server?
The tar-ing of your file is the problem here. Galaxy doesn't yet support uploading tar.gz (or just .tar) files yet. You can upload a single .gz'd file (no tar), and it will be automatically decompressed on upload.
FWIW, the extra characters at the start of the file (filename, etc) are part of the the tar header.