Question: gff to gtf conversion
1
gravatar for computationalvarun
12 months ago by
computationalvarun20 wrote:

hi i have uploaded gff format GRCh37.p13 in glaxy. however i am unable to see it on doing any analysis like for tophat and cufflink. how can i do it. how do i convert it to gtf for using it as a reference genome for tophat. it is a human genome. thanks a lot. regards

gff tophat gtf rna-seq • 862 views
ADD COMMENTlink modified 6 months ago by Guy Reeves1.0k • written 12 months ago by computationalvarun20
1

Is it really a GFF file or does Galaxy just think it is (Galaxy will label GTF files as GFF when you upload them unless you explicitly tell it that the file has GTF format)? If it's really a GTF file then just upload it again and explicitly select "GTF" as the file type.

ADD REPLYlink written 12 months ago by Devon Ryan1.7k

thank you devon. i will try again. in tophat using full parameter list i am choosing use gene annotation model. in that it is not showing grch37 although it is showing it in my history of galaxy account. i hav echosen hg19 as reference genome. how to go about it. thanks

ADD REPLYlink written 12 months ago by computationalvarun20
1
gravatar for Guy Reeves
6 months ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

There is a Tool that does this now

https://toolshed.g2.bx.psu.edu

I used it to change a .GFT file to a .GFF3 file. But I think it goes the other way.

It is on usegalaxy.org

Cheers Guy

ADD COMMENTlink written 6 months ago by Guy Reeves1.0k
0
gravatar for Jennifer Hillman Jackson
12 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

There are no tools to transform between these three formats: GFF, GTF, or GFF3.

Double check the actual file type and reload as Devon suggests or change the assigned datatype directly to be correct and recognized by tool forms as appropriate input.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 12 months ago by Jennifer Hillman Jackson23k

thank you jen. i will try the same.

ADD REPLYlink written 12 months ago by computationalvarun20
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