[Genome] liftAll.zip

[Brooke Rhead]

Hello Tam,

We do not have a liftAll.zip file for mm8.  However, nearly identical 
information is available in the 'ctgPos' table.  To get to it, make the 
following selections in the Table Browser:

clade: vertebrate
genome: mouse
assembly: Feb. 2006
group: mapping and sequencing tracks
track: map contigs
table: ctgPos
region: genome
output format: all fields from selected table

The first few rows should look like this:

#contig		size		chrom	chromStart	chromEnd
NT_039169	19418419	chr1	3000000		22418419
NT_039170	52567978	chr1	22420785	74988763

In comparison to the liftAll.zip file, these results are missing the 
chromosome sizes.  The sizes are available in the table 'chromInfo', 
which you can get from the Table Browser with these settings:

clade: vertebrate
genome: mouse
assembly: Feb. 2006
group: all tables
database: mm8
table: chromInfo
output format: selected fields from primary and related tables

hit "get output" and choose the 'chrom' and 'size' fields.

Now you should have all of the information available in the liftAll.zip 
file (but not quite in the same order).  You will need to re-order the 
columns and change the contig name format so that includes the 
chromosome number (NT_039169 will become 1/NT_039169) to get the exact 
same format as liftAll.zip.  You can use your own tools for this, or the 
tools available at Galaxy: http://main.g2.bx.psu.edu/ .

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Sneddon, Tam (NIH/NLM/NCBI) [E] wrote:
> Hi:
> 
> Do you have a 'liftAll.zip' file for mm8 in the 'Full data set' like you
> do for human?:
> 
> http://hgdownload.cse.ucsc.edu/goldenPath/hg17/bigZips/
> 
> Thanks,
> 
>  
> 
> Tam
> 
> ____________________________
> 
>  
> 
> Dr Tam Paterson Sneddon
> 
> Staff Scientist
> 
> DHHS/NIH/NLM/NCBI
> 
> 45 Center Drive - Natcher Building
> 
> Building 45, Room 5AN18D-29
> 
> Bethesda, MD 20892
> 
>  
> 
> sneddont at ncbi.nlm.nih.gov
> 
>  
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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