Question: Uploading local files to create valid datasets for analyses
0
gravatar for zhalford
7 weeks ago by
zhalford0
zhalford0 wrote:

Hi, so very new to this...

I have tried a number of different file types to upload - the tools of analysis that I'd like to use all have said "no dataset available."

What do I need to do differently to get these files once sucessfully uploaded, "available"?

upload galaxy • 109 views
ADD COMMENTlink modified 4 weeks ago • written 7 weeks ago by zhalford0

Hey, so I'm trying to basically use galaxy to unzip my gVCF.gz files -- i guess by uploading them and "converting" them to VCF files...

The issue is, I only have the option to covert it to tabix.

Even if I wanted to use the VCFtoTab-delimited tool, I cannot - it requires VCF.

What should I do? Ultimately I'm trying to take the genomic variant and non variant calls file, and sort them in in a tab-delimited format by coordinate.

ADD REPLYlink written 4 weeks ago by zhalford0

That isn't even the right file type i'm looking for.

I'm trying to figure out how to create a tab-delimited, coordinate sorted, file type that displays the depth at each coordinate included in the .bed file.

What file can I start with and what tools, if possible, can I use to modify to get the intended result I need?

ADD REPLYlink written 4 weeks ago by zhalford0
0
gravatar for Jennifer Hillman Jackson
7 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

For the compressed vcf data, it was given the datatype vcf_bgzip. Most tools will require uncompressed vcf format. You can uncompress these data at by clicking on the "pencil icon" in the upper right corner for the datasets. The Edit Attributes functions include a tab for "Convert" - you'll be converting to vcf. This is not the same as changing the datatype to vcf (under the tab "Datatype") -- changing the datatype only will create a mismatched datatype versus actual file format problem and trigger downstream tool errors.

For the compressed tar archive, please know that Galaxy does not support uploading/unpacking tar data. Data in tar archives should be uncompressed/unpacked locally and the individual files uploaded to Galaxy.

FAQ & Tutorial help: https://galaxyproject.org/support/ && https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 weeks ago by Jennifer Hillman Jackson25k
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