Question: genome coordinates hg19 from UCSC genome browser
0
gravatar for mag
4 weeks ago by
mag10
boston
mag10 wrote:

Dear all, I need a chromosome's basepair start and basepair end points (genetic locations) or in other words genome coordinates (hg19) from the UCSC genome browser, can anyone help me? how can I find it?

Thanks

genome • 136 views
ADD COMMENTlink modified 4 weeks ago by Alex Reynolds31k • written 4 weeks ago by mag10

Thank you @emilyprice, I couldn't see all start and endpoints. Is that link list all the points? Here is some part of the list from the link,

chr1 249250621

chr2 243199373

chr3 198022430

....

chr6_ssto_hap7 4928567

chr6_mcf_hap5 4833398

ADD REPLYlink written 4 weeks ago by mag10

The start is 1 and the end is the number next to the chromosome name.

ADD REPLYlink written 4 weeks ago by Hamid Ghaedi710
1

The start is actually zero; the convention is 0-based, half-open.

ADD REPLYlink written 4 weeks ago by Alex Reynolds31k

Thanks Alex. This is why I have problem with this:) :

The UCSC Genome Browser uses two different systems:

“1-start, fully-closed” = coordinates positioned within the web-based UCSC Genome Browser.

“0-start, half-open” = coordinates stored in database tables.

ADD REPLYlink written 4 weeks ago by Hamid Ghaedi710
1

What UCSC visualizes in its browser uses a 1-based index, because most of us have ten digits on our hands and that makes counting of things more "natural" in a visual rendering.

What UCSC publishes as datasets are usually (not always, but generally) zero-based, half-open, which helps make distance calculations done via scripts or programs more "natural".

When you want to know how long something is, or how far away it is from something else, it is usually easier to subtract a pair of numbers, than it is to subtract and then add one base to correct the result.

ADD REPLYlink written 4 weeks ago by Alex Reynolds31k
1
gravatar for emilyprice16
4 weeks ago by
emilyprice1620
emilyprice1620 wrote:

You can find them here: https://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes

ADD COMMENTlink written 4 weeks ago by emilyprice1620
0
gravatar for Alex Reynolds
4 weeks ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

A good, generic way to do this is to get the fetchChromSizes tool from the UCSC Kent utilities kit:

$ fetchChromSizes hg19 | awk -v FS="\t" -v OFS="\t" '{ print $1, "0", $2; }' | sort-bed - > hg19.bed

You can use this for hg19, hg38, mm10, etc. Just swap out the assembly name.

Using BEDOPS sort-bed will give you a sorted, 0-indexed BED file ready for set operations.

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Alex Reynolds31k
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