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Bedtools merge messing chromosome start - end points

Hello everyone,

I am trying to merge my bedtools genomecov output using the bedtools merge option. I am using this data :

Chromosome_1    0   54  0
Chromosome_1    54  204 3
Chromosome_1    204 410 0
Chromosome_1    410 476 2
Chromosome_1    476 502 4 ....

I used the following command to run: 

' bedtools merge' -i input.sorted.bam -c 4 -o mean > output. coverage

Here is the output: 

Chromosome_1 0 7841240 48.9278333
Chromosome_10 0 9941773 17.7389834

I am expecting to get: 

Chromosome_1 0 7841240 48.9278333
Chromosome_2 7841240 x  23.9494951

Can anyone please suggest a way to do it?

TIA!

genome merge bedtools merge bedtools
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updated by Jorge Amigo Jorge Amigo • written by nitinra • nitinra

2 answers

Can anyone please suggest a way to do it?

use sort -t $'\t' -k1,1V -k2,2n or bedtools sort with option -g

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written by Pierre Lindenbaum Pierre Lindenbaum

bedtools merge does not mess around with your chromosomes. In fact if you use it with bedfiles it expects them to be previously sorted with sort -k1,1 -k2,2n, therefore chromosomes end up being sorted as 1 10..19 2 20..22 MT X Y.

If you need some other sorting, just provide it yourself at the end of your command as Pierre suggested:

bedtools merge -i input.sorted.bam -c 4 -o mean | sort -k1,1V -k2,2n > output. coverage
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written by Jorge Amigo Jorge Amigo

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