Questions tagged [bed]

Browser Extensible Data, a collection of related plain text formats for describing genome features for visualization with genome browsers.

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19 votes
7 answers
16k views

How to convert FASTA to BED

I have a FASTA file: ...
SmallChess's user avatar
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10 votes
4 answers
265 views

Annotation format design

Bashing file formats is a favorite pastime in bioinformatics, and annotation file formats such as GFF and BED seem to get special attention. A lot of this frustration stems from community's shockingly ...
Daniel Standage's user avatar
9 votes
2 answers
726 views

How to import a large amount of .bed, .gff, .vcf, .paf, .sam files into an SQL database?

Are there best practices to load different bioinformatics file formats such as VCF, BED, GFF, and SAM to SQL databases? I am wondering how people out there do that efficiently. All of these three ...
0x90's user avatar
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8 votes
5 answers
3k views

Merging bed records based on name

I generated a file starting with the following bed lines: ...
bli's user avatar
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1 vote
2 answers
2k views

Create BED file from list with gene symbols

Is there a way to generate a BED file of a list of gene symbols for a given genome?
justinian482's user avatar