I'm new to Galaxy, and I and trying to use the "extract genomic dna" tool. I would like to fetch the sequences defined in a cuffmerge output file (GTF format) from a custom genome file in my history (an indexed fasta file, genome.fa.fai). This is the same genome file that was used in the transcript assembly through TopHat, Cufflinks and Cuffmerge, The GTF seems ok - I can successfully view it in the Integrated Genome Browser. However, when I try to run "extract genomic DNA" I get the following error after a couple of minutes:
"Error running faToTwoBit. Expecting '>' line 1 of /galaxy-repl/main/files/010/529/dataset_10529575.dat"
Any help would be greatly appreciated!