Question: uploading fastq in galaxy
0
gravatar for A
4.3 years ago by
A3.6k
A3.6k wrote:

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?

galaxy fastq sra • 1.9k views
ADD COMMENTlink modified 4.3 years ago by Matt Shirley9.2k • written 4.3 years ago by A3.6k
3
gravatar for Devon Ryan
4.3 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

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).

ADD COMMENTlink written 4.3 years ago by Devon Ryan93k

thanks Devon,

i created account already but there are illuminafastq option not fastq option, then i dont know how to upload fastq files from my computer

ADD REPLYlink written 4.3 years ago by A3.6k
2

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.

ADD REPLYlink written 4.3 years ago by Devon Ryan93k
2

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.

ADD REPLYlink written 4.3 years ago by Peter5.8k

thank you Peter

ADD REPLYlink written 4.3 years ago by A3.6k

thank you Devon for clarifying

 

ADD REPLYlink written 4.3 years ago by A3.6k
1
gravatar for Matt Shirley
4.3 years ago by
Matt Shirley9.2k
Cambridge, MA
Matt Shirley9.2k wrote:

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.

ADD COMMENTlink written 4.3 years ago by Matt Shirley9.2k

thanks Matt,

anyway today i was waiting to upload a fastq file in galaxy but never finished file was just 2 gb...i don know why it takes too long even never uploading a fastq file to galaxy

ADD REPLYlink written 4.3 years ago by A3.6k
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