I am having issues running TopHat 2. I have added the reference genome fasta file and corresponding gtf file from UCSC to my history in Galaxy for Mouse (mm10). When I look closer at the 2 files, they are both from Ensembl and have the same notation (chr1), however when I run TopHat 2 I get an error stating: Couldn't build bowtie index with err = 1.
The first line of each file looks like this:
>mm10ensGene_ENSMUST00000086465 range=chr1:134199223-134235431 5 'pad=0 3' pad=0 strand=- repeatMasking=none
chr1 mm10_ensGene stop_codon 134202951 134202953 0.000000 - . gene_id "ENSMUST00000086465"; transcript_id "ENSMUST00000086465";