genome.txt

chr1  10

surtlab.sh

# 1. convert dpeths file to bed (start is 0-based)
awk -v OFS="\t" '{print $1,$2-1,$2,$3}' toy.depths.txt > toy.depths.bed

# peek
head toy.depths.bed
chr1	0	1	5
chr1	1	2	4
chr1	2	3	3
chr1	3	4	2
chr1	4	5	1
chr1	5	6	10
chr1	6	7	20
chr1	7	8	30
chr1	8	9	40
chr1	9	10	50

# 2. make a BED files of 5bp (or 1000 in your case) intervals
# This requires a "genome" file which defines the length of each chromosome, so that it knows how many windows
# to make for each chromosome. See "genome.txt", each chrom is a line and second column is length of the chrom
bedtools makewindows -w 5 -g genome.txt > genome.5bp.bed
cat genome.5bp.bed
chr1	0	5
chr1	5	10

# 3. "map" (intersect, but with the ability to summarize data from the intersections)
# the window file with the depths file and compute the mean of the 4th column from
# the depths file
# https://bedtools.readthedocs.io/en/latest/content/tools/map.html
bedtools map -a genome.5bp.bed -b toy.depths.bed -c 4 -o mean
chr1	0	5	3
chr1	5	10	30

toy.depths.txt

chr1	1	5
chr1	2	4
chr1	3	3
chr1	4	2
chr1	5	1
chr1	6	10
chr1	7	20
chr1	8	30
chr1	9	40
chr1	10	50