I've a question about my salmon results'
I have got 6 samples (3 conditions with 2 replicates each) and therefore 6 quant.sf files for each one
I want to compare my 3 conditions : A vs B , A vs C , B vs C
But for that, I need to know more details about splicing junctions and transposable elements (TEs)
I tried to import my (pseudo)bam files into IGV to try to understand how mapped reads deal with the reference transcriptome but I couldn't do it. About TEs, I don't know how I could get information about them.. I read papers but I'm still getting confused ..