How to bin a genome to different regions

Question

[Apex92]

Hi, this is my first time binning a genome, it would be great to get some help from you experts.

I have the mouse genome GRCm38.p6.genome.fa and I would like to bin this to ~2.5 million regions that are each 1000 nts long.

With a bit of online searching, I figured out probably I have to use bedtools but still not sure how should I set the parameters.

Any help will be appreciated.

[ATpoint]

bedtools makewindows, please read its documentation and then state what is unclear.

[Apex92]

Could you please provide a link? It seems that there is no detailed manual about the bedtools makewindows.

[ATpoint]

Type bedtools makewindows into your console and the help will pop up.

Answer 1

[Alex Reynolds]

You can use BEDOPS with UCSC Kentutils:

$ fetchChromSizes mm10 | awk -v FS="\t" -v OFS="\t" '{ print $1, "0", $2 }' | sort-bed - | bedops --chop 1000 - > answer.bed

If you just want nuclear and mitochondrial chromosomes from mm10, add a grep in the middle:

$ fetchChromSizes mm10 | awk -v FS="\t" -v OFS="\t" '{ print $1, "0", $2 }' | grep -v "_" | sort-bed - | bedops --chop 1000 - > answer.bed

The file answer.bed will be a properly-sorted BED file containing your bins.

Change 1000 to whatever window size that you want.

Because genomes will not divide evenly by 1000 bases, you can add -x to the bedops --chop 1000 statement if you want to leave out the trailing bin for each chromosome, which will usually be less than 1000 bases long.

[Apex92]

Dear @Alex thank you for your detailed answer. I was wondering whether it will be possible to convert the binned genome to a gtf file. I have my purpose of binning the genome here in this link C: How to make a customized gtf file for differential expression purposes

[Alex Reynolds]

BED is generally an unbound format after the third column, with some very specific exceptions, so BED-to-GTF is not straightforward. Usually you can go the other way, however; see gtf2bed for an example.

That said, going from bins in a BED file to GTF doesn't really make sense. GTF is used to represent gene annotation data. A bin is just an (empty) genomic interval that would first need annotation and curation steps to get to something that could be turned into sensible GTF.

Maybe take a look at GenePred to GTF conversion.

Alternatively, maybe tell us what you're really trying to do. Using BEDOPS/Kentutils might be the right answer, but it depends on what you're trying to do.

[Apex92]

Basically, my purpose is to make my own gtf file to be able to find the differentially expressed regions in the genome. So that is the reason I want to do the binning and then make a gtf file out of it.

[Alex Reynolds]

You can use the bin file directly as a BED file, using mapping operations via bedmap (https://bedops.readthedocs.io/en/latest/content/reference/statistics/bedmap.html). Conversion to GTF is unnecessary.