Question: Generate transcriptome fasta for RNA-seq analysis with Salmon
1
gravatar for guillaume.rbt
10 months ago by
guillaume.rbt530
France
guillaume.rbt530 wrote:

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

transcriptome rna-seq • 427 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by guillaume.rbt530
3
gravatar for h.mon
10 months ago by
h.mon24k
Brazil
h.mon24k wrote:

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

ADD COMMENTlink written 10 months ago by h.mon24k

thanks a lot for the tools!

ADD REPLYlink written 10 months ago by guillaume.rbt530

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.

ADD REPLYlink written 10 months ago by genomax63k

sorry for being unclear, I already have an annotation file

ADD REPLYlink written 10 months ago by guillaume.rbt530
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