[Genome] Precomputed TFBS for mouse

[Kayla Smith]

Hello Diego,

One of our developers has recommended this method:

If his files have a name column with unique values (each name is used
for only one item), then the UNIX sort and join programs could do
this.  The steps would be:

1. Make a sorted-by-name version of the hg17 file.  The UNIX command
sort -k can do this.  For example, in a BED file the name is in the
4th column so "sort -k4,4" would do the trick.

2. Similarly, make a sorted-by-name version of the hg18 file.

3. Run join -j <nameColumnNumber>, e.g. join -j 4 for BED, with -o and
an output format suitable for the input files (man join to see the
format and other options).


I hope this information is helpful to you.  Please don't hesitate to 
contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group

Diego Miranda wrote:
> Hello,
> 
> I was using the downloadable liftOver facility under Linux--the program
> works perfect. However, since n input lines may map to n-m coordinates plus
> m mismatches, how do I reconstruct it? Is there a way I could make liftOver
> give me e.g.
> 
> chromosome   hg17_start  hg17_end   mapto:hg18_start  mapto:hg18_end
> 
> Many thanks, 
> 
> With best wishes from Cambridge,
> 
> diego
> 
> On Nov 8 2007, Kayla Smith wrote:
> 
>> Hello Diego,
>>
>> We do not have any plans to create a TFBS track for the mouse.  One 
>> thing you might try is our liftOver utility 
>> (http://genome.ucsc.edu/cgi-bin/hgLiftOver), to convert human TFBS 
>> coordinates to mouse coordinates.
>>
>> The details page from the human TFBS track has detailed information on 
>> the generation of this track, and a link to Biobase, which might be 
>> useful to look into: 
>> http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=tfbsConsSites
>>
>> I hope this information is helpful to you.  Please don't hesitate to 
>> contact us again if you require further assistance.
>>
>> Kayla Smith
>> UCSC Genome Bioinformatics Group
>>
>>
>> Diego Miranda wrote:
>>> Hello,
>>>
>>> I am in need of the precomputed TFBS for the mouse genome (same format 
>>> as they are provided for the human genome). I guess they are not 
>>> available on the UCSC Genome Browser....would you have them somewhere 
>>> for me, please?
>>>
>>> Thanks a lot for your help.
>>>
>>> With best wishes from Cambridge,
>>>
>>> diego
>>>
>>>
>>
>