I'm trying to investigate splicing events in RNA-seq experiments over multiple libraries.
STAR got a
SJ.out.tab output file listing splicing events over one library.
After alignments I got one
SJ.out.tab per library.
I would like to face splicing event counts between libraries, but libraries do not have the same amount of mapped reads, which lead to an impossible comparison.
Is it a way to normalize this kind of count. Something else than divide by the library size ?
Running featureCounts then DESeq2 to get a sizeFactor to apply to my splicing event counts ?
I'm aware about some multiple bias engaged in RNAseq experiment
genes length: I want to compare gene1 against gene1 in different conditions so it's OK
genes GC composition: I want to compare gene1 against gene1 in different conditions so it's OK
RNA population composition for each condition: Biologically, I expect no variation in the amount of expressed genes,only more or less splicing events
batch effect: The design is a bit messy, but I'll just ignore it for now (I'm in the exploration step)
Library size: Experiments took place in different ships so the library size are very different
Edit : I'm not looking for gene isoforms. I'm more interested in gene recombinaison (around 170 000 bp) as I'm working with B cells.