RNA-Seq plants

Question

[umeshtanwar2]

Hi all,

I am working with Barley plant and I have to do transcriptome analysis. I would like to look for differential gene expressions in treatment vs control. I am a little confused as which genome I should use for mapping. I will use STAR generating genome indexes. pseudomolecules_assembly.dna.toplevel.fa.gz or pseudomolecules_assembly.dna_sm.toplevel.fa.gz ?

https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-55/plants/fasta/hordeum_vulgare/dna/

Also what annotations are good, GTF or GFF ?

Thank you.

[jv]

There should be any difference in the information provided in a GFF versus a GTF - these two file type only differ in subtle format differences. That said, building an index with STAR uses a GTF file.