Problem while executing bedtools sort
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13 months ago
anasjamshed ▴ 120

I want to execute

bedtools sort -i S2.bed -g sizes.txt

my genome file(sizes.txt) looking like:

genome

But I am getting the following error:

Chromosome "1" undefined in sizes.txt

Can anyone help me to solve this problem? Can anyone provide me proper file with chromosome names?

genome bedtools • 640 views
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In your bed file do the chromosomes have the prefix chrm? The chromosomes names should match in the bed and sizes files exactly.

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In my bed file, only chromosome numbers are present, like:

chr

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If the chromosome sizes are from the same assembly you can remove the chrm part in the size file and it should work. If you do this make sure the contig names match between them too.

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