I got a strong 5' bias. First positions in a transcript have a high( very high coverage) . The window that follows has almost no reads.
I believe the figure should speak for itself. I join also the parameters file used.
I noticed that accepting variability in TSS position reduces this bias but I want to simulate data with a fixed TSS.
Any suggestions on how to reduce this bias?
## RT parameters
## PCR / Filtering
## no [GC] bias to not observe sequence based biases