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Question: GTF file is not recognized
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gravatar for jcoelhosilveira
4.1 years ago by
jcoelhosilveira • 0
Brazil
jcoelhosilveira • 0 wrote:

Hello,

I am trying to align my hits with a GTF file that I upload from Ensembl, however it is not being recognized. Am I missing something? Once I select the option to align to a annoyed genome, the little icon doesn't work and my file is not recognized.

Thanks

 
rna-seq referencedata gtf cufflinks inputs • 1.9k views
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modified 4.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.1 years ago by jcoelhosilveira • 0
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gravatar for Jennifer Hillman Jackson
4.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Unless you are using a custom reference genome that aligns with this Ensembl reference annotation, you will likely run into a reference genome mismatch problems. There are methods to alter the genome chromosome identifiers for certain genomes that are identical between UCSC/Alternate source and Ensembl, but not in all cases.

A bit more about reference data and why this is important:
http://wiki.galaxyproject.org/Support#Reference_genomes

And help with RNA-seq and Custom reference genomes:
http://wiki.galaxyproject.org/Support#Custom_reference_genome
http://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq

All of that said, if you still wish to use this dataset, the problem is most likely format. The proper datatype aka "format" must be assigned and in many tools, the correct reference genome aka "database". Double check these setting and adjust as needed.
http://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

Take care, Jen, Galaxy team

 
ADD COMMENT • link written 4.1 years ago by Jennifer Hillman Jackson ♦ 25k
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