uploading fastq in galaxy

Question

[zizigolu]

sorry guys,

i am in ribo-galaxy now...in get data part no option to upload a fastq file to pre-processing such as adapter trimming...i can load sra files there but no option to convert sra to fastq...then how i can start my analysis please?

Answer 1

[Devon Ryan]

Most public Galaxy instances only provide a subset of tools. ribo-galaxy provides an option to upload files (I don't see an FTP option, but perhaps one has to create an account to see that), so you'll need to just upload fastq files. Note that uploading via a web browser will limit the file sizes you can use to ~2 gigs (thus my mention of ftp).

[zizigolu]

Thanks Devon,

I created account already but there are illuminafastq option not fastq option, then I don't know how to upload fastq files from my computer

[Devon Ryan]

Those options are poorly named. The various types of "fastq" just denote the quality range. Anything made these days will be "sangerfastq", regardless of whether it's from an Illumina machine or ion torrent or something else.

[Peter]

Yes, you'll likely just want "Sanger FASTQ" encoding nowadays. See http://dx.doi.org/10.1093/nar/gkp1137 for an explanation of where these names came from.

[zizigolu]

Thank you Peter

[zizigolu]

Thank you Devon for clarifying

Answer 2

[Matt Shirley]

It looks like you have an acceptable solution, but since you mentioned using SRA archives, I'm going to point out the SRA-tools Galaxy tools: https://github.com/mdshw5/sra-tools-galaxy. You might write to the maintainers of the Galaxy server you are using, since these tools might be more efficient (for both parties) than uploading fastq from your computer.

[zizigolu]

Thanks Matt,

Anyway today I was waiting to upload a fastq file in galaxy but never finished file was just 2 gb. I don't know why it takes too long even never uploading a fastq file to galaxy