search

uschwartz / nucMACC

Pipeline to call hyper and hypo accessible nucleosomes and nucleosomes with non-canonical structure based on differential MNase-seq data
MIT License
3 stars 1 forks source link

How to define NDR #10

Closed mengqingren closed 1 month ago

mengqingren commented 2 months ago

Dear Dr, I'am wondering how to determine the NDR in nucMACC, whch module will output the NDR information. And if I want to compare the two conditional files including treated and ctrl with correspongding input files. Is it enough to obtain the DE nucleasome by running numMACC. Thank you Best

uschwartz commented 2 months ago

Hello,

Thank you for reaching out.

There is no specific function in the nucMACC pipeline to determine NDRs. Using nucMACC will mainly result in nucleosome position annotation and further nucleosome feature characterisation of accessibility (nucMACC scores) and stability (sub-nucMACC scores).

However, you could use the results to further define NDRs. Our strategy is to first select only expressed genes and then split them into 2 groups: 1) contains an unstable nucleosome directly upstream of the TSS and 2) there is none -> NDR group

Regarding the second question: Yet there is no statistical test implemented to compare two conditions and define differential nucleosomes. However you could analyse the two conditions separately and compare the output with each other. You can finde examples here [DOI: 10.1126/sciadv.adm9740] ( https://doi.org/10.1126/sciadv.adm9740 ).

best regards, Uwe