Hello I'm new in using TopHat for RNAseq data analysis I'm trying to align fastq files that generated from wheat (Triticum aestivum) samples but unfortunately it is not listed as a choice in "reference genome" select panel. So dose any one has a solution to overcome this step? Thanks in advance
Hello, are you on your own local instance ? In this case, you need to use the data manager to create genome references that will be used by Tophat. The data manager of bowtie2 allow you to make the genome available for TopHat. Hope this will help you.