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Question: How to generate a tab limited genome co-odinate file from a reference - bedtools
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gravatar for nitinra
5 weeks ago by
nitinra • 10
nitinra • 10 wrote:

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.
snp bedtools genome • 130 views
ADD COMMENT • link •
modified 5 weeks ago • written 5 weeks ago by nitinra • 10
1

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.

ADD REPLY • link written 5 weeks ago by GenoMax ♦ 95k
2
gravatar for lieven.sterck
5 weeks ago by
lieven.sterck ♦ 9.5k
VIB, Ghent, Belgium
lieven.sterck ♦ 9.5k wrote:

have you looked around on the forum already?

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

ADD COMMENT • link written 5 weeks ago by lieven.sterck ♦ 9.5k

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

ADD REPLY • link written 5 weeks ago by nitinra • 10
1

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

ADD REPLY • link written 5 weeks ago by ATpoint ♦ 44k
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