fastq vs fastqsanger

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What is the difference between the two?
how can i convert my je-demultiplexed files that are fastqsanger to fastq?

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Hi @biostaring
fastqsanger is datatype for FASTQ files with Phred33 quality score encoding used in these days practically by all sequencing technologies. fastq datatype in Galaxy is used for FASTQ data with either unknown quality encoding or for old and obsolete illumina Phred64 encoding. Very few tools in Galaxy can handle fastq datatype. If the data was generated recently, a proper datatype is fastqsanger or fastqsanger.gz. Galaxy support gz compressed data.
Hope this answers the question.
Kind regards,
Igor

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Thank you that is helpful. Is there a way to convert to FASTQ as I would like to submit the data as FASTQ for publication.

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The datatype fastqsanger is a specific type of fastq.
The datatype fastqsangergz is the compressed version of fastqsanger.

No data transformations are needed if you wish to only specify that the data is in fastq or fastq.gz format. Only the extension at the end of the file needs to be modified. You can do that within Galaxy or (usually better) outside of Galaxy after downloading the file.

The most important item to check is to make sure that if the file is in a compressed format (gz or bgz), the extension also specifies that the file is compressed, and how. The Galaxy assigned datatype can be used for reference. If you directly specified the datatype, run the dataset through the “autodetect” datatype function to confirm. The file name is not considered in Galaxy – that is just a label – the datatype metadata informs what the actual content/compression state is.

FAQs – Start here: Galaxy Training! then search that entire page at the GTN website with you browser’s find function with the keyword “fastq” to find all. These include detailed descriptions of the fastq format variations, plus how to transform (example: compressed to uncompressed, or the reverse). Galaxy Training!

I also added a few tags to this topic that link to prior QA. Or, you can search this forum directly with keywords.

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