Salmon for RNAseq alignement?

Question

[Cristina]

Hi everyone!

I'm new in this world of transcriptomics and need some help. I have the .fastq files from an RNAseq experiment, there are filtered through fastp in default settings. Someone suggested that I can use Salmon to align my .fastq files to the reference genome (I'm working with a bacteria), but I was under the idea that Salmon only works with a reference transcriptome. So, which tool do you recommend for alignment with a bacterial reference genome? Can I use Salmon to quantify my count reads?

Thanks in advance!

[GenoMax]

but I was under the idea that Salmon only works with a reference transcriptome

That is more or less correct. One could use STAR to produce a genome aligned BAM in transcriptome space (you will need to provide a GTF file when aligning) and then that BAM can be used with Salmon.

You could simply create a set of transcripts for your bacterial genome by translating the ORFs and then use them with salmon.

Answer 1

[Buffo]

Salmon is not an aligner, it is used to quantify transcripts (given a reference). If you want to align/map fastq reads to a reference genome you can use STAR, Hisat2, Bowtie2, etc.