Creating a bed file from a de novo fasta file

Question

[c.e.chong]

Hi all,

I need to create a bed file from my fasta files (from de novo assembled Metagenomic samples). I want the contig name in one column, then the start position and end position.

Does anyone have any advice on how to do this?

Thanks in advance!

[Ram]

By start position and end position, do you mean 1 and length(sequence) for each contig? You should be able to use bioawk to get that information.

[c.e.chong]

I don't want the length of the contig just the bp number where they start and end

[Ram]

Where is that information stored in the FASTA file?

[c.e.chong]

I’m not sure, that’s why I’m asking if it’s possible to do this as I was told this was the file I needed!

I’m not clear on what you mean by 1 and length(sequence)?

Thanks

[Ram]

as I was told this was the file I needed

There lies the problem. I think you need to spend a little more time understanding the problem. Talk to the person who told you this and ask them for more information.

[c.e.chong]

Thanks for your help I have a bio python script to do this now.

[colindaven]

Perhaps this would have helped with the names and lengths somewhat faster. Then adapt to BED format

samtools faidx your.fasta
cat your.fasta.fai