I am working on an RNAseq project and have successfully run cufflinks using the Ensembl Homo_sapiens.GRCh37.75 GTF file. In order to run cufflinks, however, I had to turn off the bias correction. If I want to include the bias correction in my analysis, do I need to import the Ensembl FASTA files? If so, is there an easy way to retrieve these files through Galaxy?
My understanding is that once the Bias Correction is turned to YES, I will need to specify if the FASTA files are locally cached or in my history. Is it correct that I select history only if I upload the FASTA files manually?
Any help is greatly appreciated!