Question: gtf file error
gravatar for Vijay Kumar
2.3 years ago by
Vijay Kumar20
Vijay Kumar20 wrote:

Dear all, My reference genome is Duck, not index in Galaxy reference genome. So i downloaded fasta format of duck genome from Ensembl database and i also did mapping with this fasta file by using HISAT, upto this level going fine. However while cufflinks step, my duck gtf ( downloaded from same Ensembl database) file not recognized my Galaxy as gtf file. How can i annotate my mapping results file? Kindly help me.

rna-seq galaxy • 942 views
ADD COMMENTlink written 2.3 years ago by Vijay Kumar20
gravatar for Devon Ryan
2.3 years ago by
Devon Ryan1.9k
Devon Ryan1.9k wrote:

Have you tried manually changing its datatype to "GTF" (click on the pencil in the history item)?

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Devon Ryan1.9k

Yes, i found the mistake, while uploading file instead of selecting auto detect option, selection gtf file manually, galaxy now recognizing gtf file. Otherwise it recognize as gff file. Thanks for your hints, i solve the problem .Thank you once again.

ADD REPLYlink written 2.3 years ago by Vijay Kumar20

Hi - If you have time, please accept Devon's reply, since it helped you, to help other users identify answers that resolved the original question. Do this by hovering over the left side of the question and clicking on the checkmark. Thanks! Jen, Galaxy team

ADD REPLYlink written 2.3 years ago by Jennifer Hillman Jackson25k
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