I'd like to get some advice about analyses I'd like to improve.
I'm concerned about bias (GC in particular) when comparing transcripts and gene expressions between groups of samples.
My objective are:
- Identify DE genes and DE transcripts
- Eliminate some bias before doing eQTL and sQTL mapping
About my data: 80 libraries in each of the two groups, ~30M reads in single end
Currently, I directly use the output from RSEM and pipe it to Voom to correct for known batch effects between samples (mainly flowcells effects).
Could you please point me to a better direction than this ?
Should I apply tximport before ?
Would you method, Alpine, work in my case (can it work with single end)?
Thank you for your help,