about the results

[ly Andy]

Dear developers,

Thanks for your excellent DANPOS. I have a confusion about the results hope you can give some advice. 

Using the command "dpos", I achieved the result file "*.positions.integrative.xls" that showed the number of nucleosome is 68109. The command "dtriple" also gave me the result file "*.positions.integrative.xls", but the number of nucleosome is 36084. I don't know why it is a big difference between these two results. 

Any suggestions are appreciated. Thanks in advance.

Best,

Andy

[subhashini...@gmail.com]

Dear Andy,

We had used DANPOS3 a few months back and had run both the dpos and dtriple functions. We observed differences in the number of nuclesome positions called when using these functions. We tried to find the reason for this and came up with the following explanation:

We checked the commands of the dpos and dtriple runs and all the default parameters that would have been applied in the runs. We observed that the dpos and dtriple function defaults for two parameters (--height and --pheight ) were different although as per danpos documentation they should be the same. The dpos default for the --height and --pheight parameters were 5 and 0 respectively, and this is reflected in the danpos dpos documentation. 

https://sites.google.com/site/danposdoc/b-documentation/1-dpos/parameters?authuser=0

The dtriple default for --height and --pheight parameters were 0 and 1e-10 respectively, and these are the defaults for running dpeak and dregion functions

https://sites.google.com/site/danposdoc/b-documentation/2-dpeak/parameters?authuser=0

There is no separate danpos documentation for dtriple; it simply refers the reader to dpos/dpeak/dregion parameters. The definitions of --height and --pheight as per the danpos dpos documentation is as follows:

-p , --pheight        occupancy (reads density) P value cutoff for defining individual protein binding position. Setting to a value 0 will disable this parameter and use the parameter -q or --height as an instead (default: 0)

 -q , --height         occupancy (reads density) cutoff for defining individual protein binding position. Setting to a value 0 will disable this parameter and use the parameter -p or --pheight as an instead  (default: 5)

So, in short, we think that the difference in the number of called nucleosomes is due to different default settings of --height and --pheight parameters in dpos and dtriple. Hope this helps.

Sincerely,

Subhashini and Yashoda