Question: Ensembl hg19 build GTF files recognised as.gff in galaxy
0
gravatar for saam.sedehizadeh
4.2 years ago by
United Kingdom
saam.sedehizadeh0 wrote:

I am very new to galaxy and trying to use cuffmerge with hg19 build from ensembl ftp://ftp.ensembl.org/pub/current_gtf downloading as a gtf format but when i upload to galaxy it recognises as GFF - I have tried to change to GTF in data types in edit attributes but unsurprisingly it cannot complete the task if i do this.

I know this has been discussed previously in a post: http://gmod.827538.n3.nabble.com/GTF-sniffer-td1876784.html

But simply i am not experienced enough with programming or bioinformatics to change this myself. I have used the UCSC hg19 build aswell but it would be nice if these files from ensembl work aswell.

Any help would be appreciated

Saam

gff • 2.9k views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by saam.sedehizadeh0
0
gravatar for Bjoern Gruening
4.2 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi,

you do not need to convert the file. Simply assign the right datatype to your data. Here is a little bit more information about Galaxy datatypes. https://wiki.galaxyproject.org/Learn/ManagingDatasets#Format

Cheers,

Bjoern

ADD COMMENTlink written 4.2 years ago by Bjoern Gruening5.1k
0
gravatar for saam.sedehizadeh
4.2 years ago by
United Kingdom
saam.sedehizadeh0 wrote:

Thanks Bjoern

I have already tried re-assigning the dataset's datatype attribute but then the cuffmerge tool fails to complete, so i suspect the ensembl downloaded file is almost-but-not-quite-compliant GTF file.

Any other suggestions would be very helpful

Best Wishes

Saam

ADD COMMENTlink written 4.2 years ago by saam.sedehizadeh0

Hi Saam,

do you have an error message for me :)

ADD REPLYlink written 4.1 years ago by Bjoern Gruening5.1k

Hi Bjoern

Yes here it is:

error

An error occurred with this dataset:

merge_cuff_asms v1.0.0 cuffmerge -o cm_output -p 8 -g /galaxy-repl/main/files/009/386/dataset_9386354.dat /galaxy-repl/main/jobdir/007/949/7949969/tmp0eQkxm Error running cuffmerge. [Wed Oct 8 14:55:13 2014] Beginning transcriptome assembly merge ---

Thanks

Saam

ADD REPLYlink written 4.1 years ago by saam.sedehizadeh0

Hi Bjoern

Did you manage to take a look at this?

 

Saam

ADD REPLYlink written 4.0 years ago by saam.sedehizadeh0
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