How to identify differential enhancers?

Question

[2973520704]

Deseq2 or edgeR only allow the input of reads count to identify differential regions, but I get less differential enhancer with reads count, can I use the signal from the bigwig file as input to deseq2 or edgeR to identify the differential enhancer?

[rpolicastro]

See the DiffBind or csaw documentation.

[2973520704]

Ok, thank you very much!

Answer 1

[ATpoint]

No, the scores in bigwig files are not suitable for differential expression. The exact count information, so how many independent reads overlap a given region is lost. You have to create these counts from the BAM files.