Generate transcriptome fasta for RNA-seq analysis with Salmon

Question

[guillaume.rbt]

Hi all,

I'm trying to use Salmon in a differential expression analysis, for this i need a transcriptome fasta.

Given the fact that there is only a genome available for my species, i need to generate the transcriptome (the gene annotation is available for my species, in GFF3 format).

Does anyone know a good way to do that?

Thank you in advance for you advices

Answer 1

[h.mon]

rsem-prepare-reference from RSEM ( A: Reference for Salmon ), or gffread from StringTie - I prefer the later.

[guillaume.rbt]

thanks a lot for the tools!

[GenoMax]

i need to generate the transcriptome thanks to the genome fasta and the annotation file in gff3

Unclear if you already have an annotation file or need to generate one. If you need to generate one it would not be trivial for a new genome.

[guillaume.rbt]

sorry for being unclear, I already have an annotation file