[Genome] Difference between Genome Browser and Table Browser output

[Brooke Rhead]

Hello Ko,

You did not do anything wrong, there is just a difference in formats in 
these two locations.  The Table Browser outputs conservation data in MAF 
format, described here:

http://genome.ucsc.edu/FAQ/FAQformat#format5

The numbering of coordinates on the negative strand in MAF files is 
relative to the other end of the chromosome (that is, it is relative to 
the reverse-complement of the positive strand).  So, to calculate Genome 
Browser coordinates from MAF coordinates, you need to subtract each 
start that occurs on the negative strand from the total chromosome size.

For example, the first conservation track output line for rat in the 
Table Browser (in the human (hg17) region chr12:64912201-64912645) looks 
like this:

s rn3.chr7      83636219 54 - 143082968 TCATT...

Which corresponds to:

source: rn3.chr7
start: 83636219
size: 54
strand: -
source size: 143082968

To convert these numbers to Genome Browser coordinates, first subtract 
the start from the source size:

143082968 - 83636219 = 59446749

This is the right-most coordinate displayed in the browser.  To get the 
left-most coordinate, subtract 54 from this number:

59446749 - 54 = 59446695

This is almost the exact same coordinate you see in the Genome Browser. 
  However, because MAF coordinates are zero-based and Browser 
coordinates are one-based, you need to add 1 to the start coordinate, so 
the final coordinate range becomes:

chr7:59446696-59446749

which matches the first alignment block in the shown in the Genome Browser.

I hope this explanation helps.  If you have further questions, please do 
not hesitate to contact us again.

--
Brooke Rhead
UCSC Genome Bioinformatics Group




Pang Ko wrote:
> Hi,
> 
>   I am interested in the location chr12:64912201-64912645 in human genome (hg17)
> 
>   I am using the Genome Browser with
> Genome: Human
> Assembly: May 2004
>   and choose Track Conservation to be full. Then I click on the
> conservation track and then choose rat in the multiple alignment, it
> will bring me to rat genome location chr7:59446696-59,444,569 (rn3).
> 
>   When I use Table Browser and choose
> Genome: Human
> Assembly: May 2004
> Group: Comparative Genomics
> Track: Conservation
> table: multiz17way
> Position: chr12:64912201-64912645
> 
>   The output of table browser shows an alignment with rn3 location
> chr7:83636219-83638448
> 
>   My question is why are the two output different? (one shows
> alignment with chr7:59446696-59444569 and the other shows
> chr7:83636219-83638448 in the same assembly) Did I do something wrong?
> 
> Thank you,
> Ko.
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