I hope to do DE analysis at both gene and transcript level.
First I mapped the reads to the genome using hisat2. Now I need to generate a raw count matrix for deseq2.
Since I have a well-annotated gff file, I am not interested in finding new isoforms. If I chose Stringtie, it would only be used to generate raw count matrix. And it can calculate both gene and transcript in one run (right?). If I chose Featurecounts, I have to run it twice, for gene and transcripts separately. But someone told me Featurecounts is not suitable to quantify isoforms...
What would be a better choice?