TopHat 2.1.1 and Cufflinks appear to work properly. After the tool cufflinks, the next tool in my pipeline is Cuffmerge.
In running Cuffmerge, I use the reference for human genome: hg19.fasta. I downloaded the GRCh37/hg19 full data set as a twoBit file from http://hgdownload.soe.ucsc.edu/downloads.html#human then I used the tool twoBitToFa to convert the twobit file into a fasta file (hg19.fasta).
“Use Sequence Data” answer: Yes “Choose the source for the reference list” answer: History “Using reference file” answer: hg19.fasta (from above)
When I execute, I get a red highlight saying: “the selected case is unavailable/invalid” and Galaxy stops.
Any ideas on the cause of this?