Running TopHat

[caiosuz]

Hi, fellows!
I would like to ask for your help concerning to the execution of TopHat.
I am working with reads from mRNA generated by a MiSeq machine.
Although this software had been developed for analysis of splice junctions, would it be a good idea use as a reference file a multifasta of transcripts already characterized? Or it would be better to use the wgs genome files?
Since now, thanks

[dpryan]

Don't use the transcriptome fasta file, use the whole genome fasta and a GTF (or GFF) annotation. If you want to use a transcriptome fasta then don't use tophat. Use either Salmon or Kallisto (you'd then use Sleuth for the eventual analysis).