I'm trying to run cuffdiff with mouse_ucsc_mm9 genome reference, but encountered the following error
Loading reference annotation and sequence. No fasta index found for /usr/local/bowtie_indicies/mouse_ucsc_mm9.gtf. Rebuilding, please wait.. Error: sequence lines in a FASTA record must have the same length!
The tophat/cuffliks/cuffmerge steps worked pretty well, I do not understand why cuffdiff throws errors about the genome reference. Does this mean I need to build the index of mm9? if so, what tools can I use? thanks