Defining a bedfile for chromosome X without pseudo-autosomal regions

Question

I would like to define a bedfile for chromosome X, to target only basepairs outside of pseudo-autosomal regions (and going forward other regions, too).

First, I wasn't able to find an already prepared bedfile in any of the online repositories (but let me know if it is available somewhere).

Second, I compiled the bedfile for all basepairs in chromosome X as a starting point (by looking at the latest assembly at genome browser):

chrX    0       156040895       # as defined at https://genome.ucsc.edu/

The genome browser is 1-based and the last base is inclusive, while the bedfile is 0-based and last base is not inclusive, therefore I had to subtract 1 from the bed start.

Afterwards, I wanted to exclude the pseudo-autosomal regions as defined at this page. However, I am not sure if basepair "Start" and "Stop" are 0- or 1-based and inclusive/not inclusive. I might use the same convention used on the genome browser, but I am not sure if that's correct in this case. I wasn't able to find this information on their website or online.

Assuming that the NCBI "Start" and "Stop" field follow the UCSC parameters (1-based and inclusive), the resulting bed (PAR regions excluded) might be the following:

chrX    0       10000
chrX    2781479 155701382

Edit: the section on the centromeres has the "Length" parameter, from which I could infer that "Start" and "Stop" base-pairs are both inclusive. At the same time, the "Stop" base-pair of PAR#2 in chromosome X is base-pair 156,030,895, which is also the last base-pair number if we were considering the UCSC genome browser notation (1-based and inclusive). Therefore, it seems to me clear that the same notation is used, and the proposed bed-file should be correct.

Answer 1

The UCSC Genome Browser renders data visually with a one-based, closed index. The underlying data are often stored and presented as files worked with on the command-line, using zero-based, half-open coordinates.

This difference in indexing can be important when using the website to view data or when using the download tools to grab a dataset for offline calculations, such as files in BED format.

There is a good overview of indexing on Biostars.

To solve this in a general way:

The UCSC Kent Utilities fetchChromSizes tool can be used to retrieve the sizes of chromosomes for your genome assembly of interest, e.g. hg38.

Using this assembly, to build a sorted BED file for set operations:

$ fetchChromSizes hg38 | grep -v '_*_' | awk -v FS="\t" -v OFS="\t" '{ print $1, "0", $2 }' | sort-bed - > hg38.bed

Replace hg38 with your assembly of interest.

To then filter this for chrX:

$ awk '($1=="chrX")' hg38.bed > hg38.chrX.bed

The intervals in hg38.bed and hg38.chrX.bed use a zero-based, half-open coordinate system.

To then get regions of chrX without autosomal regions, you could define a sorted BED file containing those regions, which also use zero-based, half-open coordinates:

$ echo -e 'chrX\t10000\t2781479\nchrX\t155701382\t156030895' > pseudoautosomal.chrX.bed

I am assuming that the coordinates on Ensembl and NCBI use one-based indexing. Converting to a zero-based index requires subtracting one base from the start positions of these intervals.

It would be ideal if these groups were to clarify the indexing they use. I am making this assumption based on how Ensembl defines regions on chrY, which start at position 1 and not 0, as one would expect to see with a one-based coordinate system.

The numbers reported on Ensembl and NCBI are otherwise identical, so I also assume that NCBI's numbers use the same indexing and require the same correction to the start base.

In any case, to calculate the difference between these regions and chrX:

$ bedops --difference hg38.chrX.bed pseudoautosomal.chrX.bed > answer.bed

This is what my output looks like:

$ more answer.bed
chrX    0   10000
chrX    2781479 155701382
chrX    156030895   156040895

These coordinates are in BED format and so use a zero-based, half-open coordinate system, by convention.

To turn these into one-based, closed coordinates — to query signals over exact regions in the UCSC Genome Browser, for instance — you would add one base to the start positions of each genomic interval.

(Edit: Fixed PAR#2 start coordinate per comment.)