Bed file coordinates

Question

[storm1907]

Hello, I am supposed to extend bed file coordinates by 2bp with Bedtools. I am very new to field and have a poor understanding about bed files.

The syntax with Bedtools should be like this: bedtools slop [OPTIONS] -i <bed gff="" vcf=""> -g <genome> [-b or (-l and -r)]

What are <bed gff="" vcf=""> and <genome> files in this case?

I have downloaded hg38.bed file from sequencing company's website - is that " -g <genome> " file?

Thank you!

Answer 1

[Pierre Lindenbaum]

<bed gff="" vcf="">

a BED file OR a VCF file.

 <genome>

https://bedtools.readthedocs.io/en/latest/content/general-usage.html

Some of the bedtools (e.g., genomeCoverageBed, complementBed, slopBed) need to know the size of the chromosomes for the organism for which your BED files are based. When using the UCSC Genome Browser, Ensemble, or Galaxy, you typically indicate which which species/genome build you are working. The way you do this for bedtools is to create a “genome” file, which simply lists the names of the chromosomes (or scaffolds, etc.) and their size (in basepairs).