Interpreting *.nucmap_combined.bed.gz file and downstream analyses

[obwan74]

Dear Alicia,
Thank you for developing the method and package.

I have some basic questions and confusion about terminology.

*.nucmap_combined.bed.gz - This file contains regions that are bound by chromatin

and

*.nfrpos.bed.gz - this file has nucleosome free regions.

These are one base coordinates where base where apex of the peak is reported.

For downstream analyses, such as DESeq2, to count reads for the peaks, where can I get the start and end position of the peaks. Which file should one consider for counting reads.

I am sorry, if am missing something critical due to my naivety.

Thanks
Adrian