[Genome] looking for the table containing the exact information of a side by side

[Brooke Rhead]

Hi Xiaolu,

I think what you are saying is that you would also like to see qName and 
qEnd listed in this table.  You can, as you say, get it from the 
chainMm9 table.  There is an easy way to do part of this with the Table 
Browser: first select the chainMm9Link table, then choose "output 
format: selected fields from primary and related tables".  Now you can 
select the chainMm9 table, and select the qName and qStrand fields.

The qEnd field could be generated from qStart and the information in the 
target fields.  You would need to subtract tEnd from tStart to get the 
size of the alignment, then add that number to the qStart.  I believe 
the Galaxy web site run by Penn State (http://main.g2.bx.psu.edu/) has 
tools to manipulate columns in this manner (look under the "Text 
Manipulation" header on the left-hand side of the page).

I hope this information is helpful.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Xiaolu Huang wrote:
> Dear Dr. Rhead,
> 
> Thanks a lot for the prompt reply! The information you provided is very 
> helpful. I have found the file I am looking for.
> 
> for the table of chainMm9Link. Here is the concern:
> 
> At the table brower page, I have entered "human" for genome, track 
> "mouse chain" position "chr21". and for chainMm9Link table results 
> without any filters and with all attribute information.  I have got
> 
> ************************************************************
> #bin tName tStart tEnd qStart chainId
> 935 chr21 46001419 46001439 53663552 212
> 935 chr21 46001441 46001479 53663572 212
> 935 chr21 46001488 46001514 53663610 212
> *************************************************************
>  
> At the tName, I would rather see the mouse chromosome name, and mouse 
> treated as the target and human as the query. But I can also go to the 
> chainMm9 table and get the information.
> 
> Thanks!
> 
> Xiaolu
>