I am new to STAR and new to genome guided assembly in general; I have more experience with de novo assembly.
I would like to use trinity to assemble my fastq reads against a genome assembly. Am I supposed to supply the .sam file (I guess it would be coordSorted.bam after sorting/coordinating) that was outputted after I used STAR to generate a genome index?
If yes, would I be using the Trinity parameter
Thanks for the help! Nikelle