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How to generate a tab limited genome co-odinate file from a reference - bedtools

Hello all,

I am trying to generate a genome file similar to this from a fasta reference genome. What tool can I use to generate this?

Thank you.

genome snp bedtools
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written by nitinra • nitinra

File you linked has the sizes of the chromosomes. These files are available from UCSC (if you are working with a genome there) or you can simply add up the nucleotides in your fasta file for each sequence and make that file. e.g. faslen from this.

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written by GenoMax GenoMax

1 answer

have you looked around on the forum already?

eg. this thread: Calculate length of sequences from fasta file

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written by lieven.sterck lieven.sterck

thank you so much! I don't think I was using the right keywords. I completely missed this!

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written by nitinra • nitinra

Please accept the answer if it solved the issue, it is the checkmark symbol left of his answer.

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written by ATpoint ATpoint

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