I have a large file of each chromosome for sequence data and I want to get the average score in 1kb bins? Is there an easy way to do to this?
chr1 123 127 1890 chr1 208 210 90 chr1 215 220 50 chr1 225 230 100 chr1 250 300 800
I have tried bedtools, it will create the windows but then how do I get the average of the fourth value in that window? It also seems to be quite slow.
bedtools makewindows -w 1000 -g chromosome.txt > windows.txt
Any help would be much appreciated.