I am new here so first, nice to meet to all of you.
I am a PhD Student and I have a question about tophat and the reference genome.
On one hand, I have been using the reference genome with the gtf file for the alignment with tophat. On the other hand, I have been using the coding reference genome (cDNA) for the alignment with salmon.
My question is the following:
Can I use the cDNA with tophat and the gft? Because I need the BAM files and the count with tophat for a set of data but, I am interested also in the integration of these data with the data belonging to salmon. I supposed that if the data hasn't been extracted with the same reference genome, I can't integrated them.