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?
•
written
by
alonziso •
1 answer
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.
Log in to answer this question.
-
Analyzing RNA-seq data with Salmon
written by Eduardo Oñate •
-
Using salmon on HISAT2 BAM files for transcript quantification
written by skden2020 •
-
Using Salmon to map RNA-Seq and Ribosome Profiling reads in Yeast and downstream analysis with DESe…
written by kyusikkim •
-
star alignment
written by biology_inform •
-
Good QC Package (RSeQC or alternative) for Salmon mapping/quantification results?
written by skjw1029 •
-
variant calling using pseudoaligners
written by jmgoldstein7 •
-
RNA-SEQ SNP calling
written by babji2318 •
-
PCA plot from read count matrix from RNA-Seq
written by rachel.kubik12 •
-
samtools variant calling workflow
written by mirza
-
Cufflinks invalid BAM binary header
written by murphy.charlesj
