I'm trying to run a genome-guided de novo assembly using trinity with fastq files from zebrafish RNA samples but I have never done an RNA-Seq experiment before.
In the documentation for trinity it says that you must create a coordinate-sorted BAM file for the reference genome using STAR or TopHat. I'm not sure how to go about doing this.. I have downloaded the file 'Danio_rerio.GRCz11.dna_rm.primary_assembly.fa' from Ensembl. Is this the right file to download? Also, what should I be doing with this file?
Any help is greatly appreciated!!!