salmon quantification and then generating BAM files using STAR

Question

[alonziso]

Hi, I've been doing a lot of bioinformatics lately and was asked to perform variant calling on RNA-Seq data used in my lab the thing is that I used Salmon to quantify may RNA-Seq data, and performed Differential expression analysis
now that I want to generate BAM files for the variant calling I need to use STAR the question is, do I need to perform alignment with STAR and then quantify again with salmon, or is it possible to just run with my DE analysis and just generate the BAM files with STAR for the variant calling?

Answer 1

[Michael Love]

You can't use STAR's genomic alignments with Salmon (easily).

Salmon can take in transcriptome alignments as input, but not genomic alignments.

So it's two separate tasks, but luckily these are both quite fast. We use Salmon/STAR/Hisat2 in our lab often in combination. It helps to view genomic alignments for a number of analyses, including genetic variation.