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Question: fastq convert problem
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gravatar for haniehhadizadeh63
17 months ago by
haniehhadizadeh63 • 0
haniehhadizadeh63 • 0 wrote:

Hi. I have a problem using my data on galaxy for proces radtags. First I had to trim my raw data so I used fastq trimmer on galaxy and before that I used fastq groomer to change the file type. Now I have fastqsanger files which do not match to process radtag and I need to convert them to fastq files. How can I convert fastqsanger files to fastq?

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modified 17 months ago by Jennifer Hillman Jackson ♦ 25k • written 17 months ago by haniehhadizadeh63 • 0
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gravatar for Jennifer Hillman Jackson
17 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The datatype fastqsanger is a specific subtype of the datatype fastq. Either can be applied and which to use depends on where you are working. Within Galaxy, use the datatype fastqsanger. Outside of Galaxy (line-command), adjust the file extension to be .fastq.

Format help within Galaxy: https://galaxyproject.org/support/#getting-inputs-right-

Are you using the STACKS tool suite in Galaxy (available from the Tool Shed)? This accepts fastqsanger datatype input for fastq data. For help with usage, see the tool forms, as they include links to the development website, the manual, and a help group.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 17 months ago by Jennifer Hillman Jackson ♦ 25k

Thank you for your response. I am using stacks through galaxy. I wanted to do the process radtags on my data but I received zero bytes files for all process radtag files while I used those trimmed files which are in the format of fastqsanger. I don't know it was the problem or I have another problem. Also I am not sure for barcode file we need just one column file of barcodes per lines or we need to add a second column of sample name or not?

ADD REPLY • link written 17 months ago by haniehhadizadeh63 • 0
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