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Question: uploading fastq in galaxy
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gravatar for mabitu0
3.2 years ago by
mabitu0 • 0
European Union
mabitu0 • 0 wrote:

sorry guys,

i am in ribo-galaxy now,i created account already...in get data part no option to upload a fastq file to but there is illuminafastq option not fastq option instead, then i dont know how to upload fastq files from my computer for pre-processing such as adapter trimming...i can load sra files there but also no option to convert sra to fastq...then how i can start my analysis please?
ribo-galaxy sra fastq trimming • 1.3k views
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modified 3.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.2 years ago by mabitu0 • 0
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gravatar for Jennifer Hillman Jackson
3.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

It is not clear if "fastq" or "fastqsanger" format is required by the tools on this particular server (this is not mentioned on the tool forms or in their help, or I didn't find it from a quick search). Ask in their forum for the most current information. Most Galaxy tools require fastqsanger.

Once that is determined, upload to http://ribogalaxy.ucc.ie/ server either using auto-detect for datatype assignment (this will result in ".fastq") or specify ".fastqsanger". Make sure that the data really is in fastqsanger format if you assign this.

Dataset format can be reviewed and adjusted (if needed) using the tools at http://usegalaxy.org. This is how: https://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA. 

Hopefully this helps! Jen, Galaxy team
ADD COMMENT • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k
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