Splitting chromosomes in bins of 100kb

Question

[ChIP]

Hi!

I have the genomic table file of hg19, describing the lengths of each chromosomes. How can I split it up into bins of 100kb for each chromosome.

The file looks like this:

chr1    0    249250621
chr2    0    243199373
chr3    0    198022430
chr4    0    191154276
chr5    0    180915260
chr6    0    171115067
chr7    0    159138663
chr8    0    146364022
chr9    0    141213431
chr10    0    135534747
chr11    0    135006516
chr12    0    133851895
chr13    0    115169878
chr14    0    107349540
chr15    0    102531392
chr16    0    90354753
chr17    0    81195210
chr18    0    78077248
chr19    0    59128983
chr20    0    63025520
chr21    0    48129895
chr22    0    51304566
chrX    0    155270560
chrY    0    59373566
chrM    0    16571

Any one liner in awk or perl?

Thank you

Answer 1

[slw287r]

try

bedtools makewindows

Answer 2

[Alex Reynolds]

$ awk ' \
    BEGIN \
    { \
        binSize = 100000; \
        binIdx = 0; \
    } \
    { \
        chr = $1; \
        start = $2; \
        stop = $3; \
        for (binStart = start; binStart < (stop - binSize); binStart += binSize) { \
            print chr"\t"binStart"\t"(binStart + binSize)"\tbin-"binIdx; \
            binIdx++; \
        } \
    }' chrExtents.bed \
    > myBins.bed

Answer 3

[Vivek]

awk '{for(i=1; i<= $3; i=i+100000) if(i < $3 - 100000) print $1"\t"i"\t"(i+100000); else print $1"\t"i"\t"$3}' file.txt