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.
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Question: gtf file error
2.3 years ago by
Vijay Kumar • 20
Vijay Kumar • 20 wrote:
ADD COMMENT • link •written 2.3 years ago by Vijay Kumar • 20
2.3 years ago by
Devon Ryan • 1.9k
Devon Ryan • 1.9k wrote:
Have you tried manually changing its datatype to "GTF" (click on the pencil in the history item)?
ADD COMMENT • link modified 2.3 years ago • written 2.3 years ago by Devon Ryan • 1.9k
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 REPLY • link written 2.3 years ago by Vijay Kumar • 20
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 REPLY • link written 2.3 years ago by Jennifer Hillman Jackson ♦ 25k
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