Analyzing RNA-seq data with Salmon

Question

[Eduardo Oñate]

Hello everyone, I want to use the SALMON tool to quantify some RNA-seq data and then perform a differential expression analysis with DESeq2 and edgeR. While reading the Salmon manual, a question arose regarding the input needed to generate the index for aligning my reads. It mentions that a reference transcriptome should be used. My question is whether I can use the files available on NCBI, which are in the formats "rna.fna.gz", "rna.gbff.gz", "rna_from_genomic.fna.gz". I ask this because some tutorials specify a file format like ".cdna.all.fa.gz", as mentioned in the following link https://combine-lab.github.io/salmon/getting_started/. I would appreciate it if someone could take the time to respond.

Answer 1

[GenoMax]

Short answer is yes. You should double-check the file to make sure that it contains transcripts/CDS (for prokaryotes). There was a recent example (prokaryotic) where a file from NCBI labeled rna only contained rRNA/tRNA.

[Eduardo Oñate]

thanks!, I will check if my files contain cdna