For my project, I have been working with Illumina RNA-seq samples and a genome assembly of my species, and one of my tasks was to improve the genome annotation and build a genome-guided transcriptome for my species.
For this purpose, I used hisat2 + stringtie2.
Recently, it has been made available to me 12 samples of RNA-seq, sequenced using MinION. My objective now is to improve my current annotation using these samples, which I already verified that contained novel transcripts.
Since I already used stringtie2, I assembled a new transcriptome using these long-reads (minimap2 + stringtie2).
My question is :
1) Should I use the --merge option of stringtie2 and merge both my Illumina transcriptome and my nanopore transcriptome? Or this is not compatible?
2) Should I use some other tool that is available (and preferably genome-guided since my objective is to improve the current genome annotation?)
Thanks in advance