I have a File that contains certain enhancer regions per chromosome and per region how many reads are found from different samples. The 1 and the 2 stand for the two different groups I have. The original file is tab delimited. I.E.:
$ cat enhancers.bed
chr | start | end | sample1a | sample2a | sample2a | sample2b
2 | 2000 | 4000 | 3245 | 2345 | 4234 | 5409
2 | 2200 | 4400 | 1842 | 2086 | 1902 | 2181
2 | 3500 | 5200 | 6912 | 6209 | 4234 | 5409
...
Now I wanted to find in which regions a certain group is deferentially active. I read somewhere that I should use DESeq2 for this, now the only problem is that I cant find anywhere how I should do this ... I haven't used R in a while and my skills in this language are very rusty... Is there someone who can help me?
Read the DESeq2 manual, it convers everything you need. Alternatives for ChIP-seq are DiffBind or csaw, both are Bioconductor packages and both have extensive documentation.