Recommendations for dealing with DEseq2 (DEGs) in non-model organism.
Hi All,
Hope you can help please:
I'm working on RNA-seq data from a non-model organism. I assembled transcripts with StringTie, performed differential expression with DESeq2, and now have a list of significant DEGs. My transcript IDs in this look like MSTRG.xxx|LOCxxxxxx and MSTRG.xxx.
I have the stringtie_merged.gtf, the reference genome FASTA and DESeq2 results.
I'm now at the annotation and functional analysis stage. What annotation tools/ r packages have people found work best for this type of dataset? I am considering blasting everything, but would be interested to hear what others use?
Also for downstream functional analysis, what do people recommend for GO and pathway enrichment? Are there particular R packages or workflows that work well with StringTie/DESeq2 output of a non-model.
Thanks in advance for all your help.