Re: [galaxy-user] How can I extract sequence information fromm cuffdiff files?

Hi Humberto, Yes, my apologies, this should have been included in the original reply. The 'locus' field in the Cuffdiff files refers to a gene bound - not individual transcripts. To get to the transcripts, the inputs to Cuffdiff need to be accessed. If you used Cuffmerge, the "merged transcri

Re: [galaxy-user] How can I extract sequence information fromm cuffdiff files?

Hello, By no annotation, do you mean species-specific annotation (GTF) was not used? And you want to compare to a protein database like Genbank NR or RefSeq? Then these are the instructions. Please let us know if you had something else in mind. The sequence extraction can be done on Galaxy M

[galaxy-user] How can I extract sequence information fromm cuffdiff files?

Hi. I got cuffdiff files with gene differential expression on it. I don't have the annotation, therefore I need to extract the sequence information from the genome coordinates and them blast them to identify those. How the easiest way to do it? Thanks. Humberto Dr. Humberto Boncristiani Nat