I am relatively new to the field. I would be very grateful to have second opinion on below options from someone with STAR and HTSeq experience (particularly in the context of AT or plant species).
## My ReadLength-1
## log2(GenomeLength)/2 - 1=12.41
--outSAMtype BAM Unsorted
## 99.3% of introns in AT are below this size based on doi:10.3390/genes8080200
I have been trying to find the optimum settings using available literature, however the variety has been overwhelming. I eventually ended up pasting together above options from few references that appeared to be more in line with the analysis I am hoping to perform ( Which is simple DE analysis at gene level.).
Many thanks for your time and help in advance,