After performing, Hisat2-stringTie and DESEQ2 how can I identify if there are any novel mRNA transcripts present in my significant genes or if so which tool do I use? Can someone help me out here?
Thanks in advance!
Hi, I believe the novel transcripts will be assigned an automatic ID from the HISAT2-StringTie stage, depending on how you have run these programs. Please check the merged GTF that you produce with StringTie to see if any novel transcripts have been identified.
According to a colleague, the automatic ID for novel transcripts may begin with something like 'MSTRG'.
It would help if you showed the commands that you used, and also sample outputs from different stages.