DANPOS3: how to change the default size and start positions of the nucleosomes

[Alexey Kozlenkov]

Hi all,

I really hope that this user group is still active.

I have tried to use DANPOS3 to call nucleosome positions from a test BAM file of a H3K27ac ChIP-seq experiment.

I use the command like:

python danpos.py dpos -m 1 -p 1e-8 -q 0 test_bam_directory/

It generally seems to work but with some strange issues:

- The predicted size of nucleosomes is always 140bp, whatever settings I try. 

- All nucleosome start positions seem to have a step of 10bp, and always start with a coordinate ending with 1, such as in:

chr1 794511 794651

chr1 817081 817221
chr1 817271 817411
chr1 818701 818841

- also, some predicted nucleosomes overlap each other

Could anyone guide me how to modify those settings?

PS : I also thought of trying DANPOS version 2, but could not find any active link to download it.

Thanks in advance,

Best,

Alex