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Difference in chromosome numbering

I am using bedtools getfasta to extract some sequences from the reference genome, hg38. I have the bed file ready but the chromosome numbering is like 1,2,3,...,25.

In my hg38.fa, however the chromosomes are numbered from 1,2,3, ...,X,Y,Mt. This is the reason I am not able to get fasta sequences from chromosomes 23,24 etc.

How to solve this?

r next-gen bedtools fasta
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updated by zx8754 zx8754 • written by Gene_MMP8 Gene_MMP8

1 answer

Rename X,Y,MT to 23,24,25. Something like this should work:

sed -e 's/X/23/' -e 's/Y/24/' -e 's/MT/25/' hg38.fa > new.fa
• 1 views • link
written by GenoMax GenoMax

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