Statistical analysis on tags mapping in binned chromosomes intervals

Question

[mujupas]

Hi!

I have a question related to this post:

Binning Of Chromosome Data

My goal is to check whether different libraries have statistically significant differences int the density of mapped tags along the chromosomes.

I've binned the human chromosomes with bedtools makewindows, now I need to intersect the BED files derived from my libraries to these bins...but what would be the best tool/statistical analysis to test for differences in densities in each bin for different libraries?

Thank you in advance!

Answer 1

[Sean Davis]

Bioconductor edgeR and DESeq2 packages are built for doing just this. You can treat the bins as "genes" and just follow a normal rna-seq workflow.

[mujupas]

Ok, I will try them, thanks a lot!