I'm new here, so I hope I'm posting properly.
I'm using bedtools in order to know where some different epigenetic marks are present across a mouse genome split into different regions.
To do so, I used makewindows function to split the genome into 10k chunks:
bedtools makewindows -g mm9.genome -w 10000 > mm9.windows.bed
Then, I tried the intersect function like this:
bedtools intersect -a mm9.windows.bed -b H3K4m1.bed H3K4m2.broadPeak -loj -names H3K4m1 H3K4m2
but I got nothing!
There's a H3K4m1 mark with this information:
chr1 4352396 4353107 . 0 . 6.73 -1 -1
Which I guess it should have an intersection here in the genome (mm9.windows.bed):
chr1 4350000 4360000
However, I get no output!
I don't know if this is relevant, but the files I use have the following formats:
- mm9.windows.bed --> BED3
- H3K4m1.bed --> BED6
- H3K4m2.broadPeak --> broadPeak (BED9)
I would really appreciate some help because this is really getting me crazy!
All the best,