[Genome] 10,000,000 line limit

[Brooke Rhead]

Hello again Damian,

This data are now available in the ENCODE downloads area in the hg17 
Supplementary Files section, located here:

http://hgdownload.cse.ucsc.edu/goldenPath/hg17/encode/datafiles/Yale/TransMap/2005-10-14/

Sorry for all of the confusion.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Brooke Rhead wrote:
> Hello Damian,
> 
> The encodeYaleAffyNeutRNATransMap table which underlies the "Yale 
> Neutrophil RNA Transcript Map" sub-track of the "Yale RNA" track 
> actually only contains 22,633 lines (hit the "describe table schema" 
> button to get more information about the table).  However, this track is 
> a "wiggle" type track (more information on wiggle tracks is here: 
> http://genome.ucsc.edu/goldenPath/help/wiggle.html ), which means that 
> the Table Browser output formats are somewhat different from other track 
> types.  The "data points" option gives a value for every base covered by 
> the track.  The "bed format" option in this case is simply the first 4 
> bed fields from the encodeYaleAffyNeutRNATransMap table, so you will 
> likely not want to use this option.
> 
> If you want to get the entire track as "data points" from the Table 
> Browser, you will need to split up your Table Browser queries (by 
> chromosome, for instance).  If you hit the "summary/statistics" button 
> in the Table Browser when region: genome is set, you will see how many 
> data points are on each chromosome for this track.
> 
> If you are interested in getting the encodeYaleAffyNeutRNATransMap table 
> in the format you see when you hit the "describe table schema" button, 
> it is available on our downloads server, here:
> 
> http://hgdownload.cse.ucsc.edu/goldenPath/hg17/database/
> 
> The files here are text files, but they are compressed with gzip.
> 
> I hope this information is helpful to you.  Please contact us again if 
> you have further questions.
> 
> -- 
> Brooke Rhead
> UCSC Genome Bioinformatics Group
> 
> 
> 
> Damian Keefe wrote:
>> Hi
>>
>> I would like to download the entire track 
>> encodeYaleAffyNeutRNATransMap. However it contains more than 
>> 10,000,000 lines. 10000000 seems to be the maximum in the filter. Is 
>> there another way to get all the lines for this track. - I looked at 
>> the download page but the data pointed to seems to be in some binary 
>> format I can't read.
>>
>> cheers
>>
>> Damian
>>
>