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Question: Ensembl hg19 build GTF files recognised as.gff in galaxy
0
gravatar for saam.sedehizadeh
4.2 years ago by
saam.sedehizadeh • 0
United Kingdom
saam.sedehizadeh • 0 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
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modified 4.2 years ago • written 4.2 years ago by saam.sedehizadeh • 0
0
gravatar for Bjoern Gruening
4.2 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k 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 COMMENT • link written 4.2 years ago by Bjoern Gruening ♦ 5.1k
0
gravatar for saam.sedehizadeh
4.2 years ago by
saam.sedehizadeh • 0
United Kingdom
saam.sedehizadeh • 0 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 COMMENT • link written 4.2 years ago by saam.sedehizadeh • 0

Hi Saam,

do you have an error message for me :)

ADD REPLY • link written 4.1 years ago by Bjoern Gruening ♦ 5.1k

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 REPLY • link written 4.1 years ago by saam.sedehizadeh • 0

Hi Bjoern

Did you manage to take a look at this?

 

Saam

ADD REPLY • link written 4.0 years ago by saam.sedehizadeh • 0
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