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?
NB_MOLECULES 50000 TSS_MEAN NaN POLYA_SCALE 50 POLYA_SHAPE 2 ## Fragmentation FRAG_SUBSTRATE RNA FRAG_METHOD UR FRAG_NB_LAMBDA 50 ## RT parameters RTRANSCRIPTION YES RT_PRIMER RH RT_LOSSLESS YES RT_MIN 2000 RT_MAX 6000 ## PCR / Filtering ## no [GC] bias to not observe sequence based biases PCR_DISTRIBUTION default PCR_PROBABILITY 0.5 GC_MEAN NaN FILTERING YES SIZE_SAMPLING MH # Sequencing FASTA true READ_NUMBER 1000000 READ_LENGTH 50 PAIRED_END NO