Parameters, including sliding window size, step size, bootstrapping iterations, and the use of trimA1 (version 1.2) [ 37] to remove gaps, are adjustable.
ChIP-seq reads were mapped using BWA [ 84] and peaks detected using CCAT 3.0 (Settings: fragment size = 200, sliding window size = 500, minimum score = 3.0) [ 85].
In total, this yielded a total of 434 peptide sequences containing validated methylated arginines and 550 peptide sequences containing validated methylated lysines with sliding window size 11(the optimal window size for both arginine and lysine is 11 after several trials of 5, 7, 9, 11, 13, 15, 17 and data information regarding other sliding window sizes not shown here), respectively.
The d N/d S ratio of myo-sex was calculated using JCoDA using a sliding window size of 200, and a jump size of 20.
We used a sliding window size of 200 nucleotides with a step size of 20 nucleotides.
Briefly, the consecutive genotypic SNPs on each pseudomolecule were scanned with a sliding window size of 15 SNPs and a step size of 1.
In our experimental setting, the parameter q = 0. 90, the sliding window size of the median filter is 15×15 pixels, and the patch size L = 25.
The sliding window size was chosen to be 96 nt long and the step size to be 3 nt.
A buffer was then constructed for each point using a sliding variable size based on the great circle distance to neighbouring points in the grid pattern.
Setting the sliding window size is not a trivial task.
