Hello. I'm trying to analyzing RNA-seq data with DESeq2 to study differencial gene expression. I have SAM and BAM files generated by samtools. How do I insert my files on R to run DESeq2? Do I use the SAM files, BAM files or sorted BAM files?
Thank you in advance.
As you can see in the DESeq2 vignette, it requires a count matrix so you will not be able to start with your files. First you will need to create this matrix from your .bam files and you can use featureCounts in that purpose