External links to Blat result with custom tracks

[David Anchel]

Hello, I would like to include a link to a BLAT search that I have done in a manuscript for publication.  Included in the result is a custom track:

http://genome.ucsc.edu/trash/hgt/hgt_genome_5173_3ba450.png

Surprisingly it works, but I suspect that your servers periodically clean out custom tracks from your database?  Is this true?  If so is there a way to permanantly link to a BLAT output that includes a custom track?  Any help you would provide is appreciated.

David Anchel

University of Toronto

415-570-1535

[Enrique Medina-Acosta]

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[Jonathan Casper]

Hello David,

Thank you for your question about setting up a permanent link to BLAT results. You are correct that our servers periodically clean out old custom tracks from our database. The cleanup for BLAT results is particularly stringent - BLAT results are deleted after 48 hours, regardless of whether they are part of a saved session or how recently they were last accessed.

If you would like to set up a permanent link for your BLAT results for use in a publication, we suggest that you instead create a track hub that displays them. That way you will retain control over the data files related to your publication. Please note that creating a track hub requires that you have some web hosting space to make the data available; your institution can probably assist you with setting that up. The steps to create your track hub would look something like this:

1. Go to http://genome.ucsc.edu/cgi-bin/hgBlat and perform your BLAT search, but select the output format as "psl no header".
2. Copy and paste the output into a text file, and name the file something like blat_results.psl. The contents of the file should look something like this:

   142 0 0 0 0 0 0 0 + hg19_mydna  142 0 142 chr14 107349540 79234517  79234659  1 142,  0,  79234517,
   36  1 0 0 1 6 1 1 - hg19_mydna  142 1 44  chr3  198022430 178263866 178263904 3 9,16,12,  98,113,129, 178263866,178263875,178263892,
   30  0 0 0 2 6 0 0 - hg19_mydna  142 17  53  chr4  191154276 1176329 1176359 3 17,8,5, 89,109,120, 1176329,1176346,1176354,

3. Convert your PSL file to BED format using the command-line pslToBed tool (available at http://hgdownload.soe.ucsc.edu/admin/exe).

   pslToBed blat_results.psl blat_results.bed

4. Convert your new BED file to bigBed format. A description of how to do this is available at http://genome.ucsc.edu/goldenPath/help/bigBed.html.

   bedToBigBed blat_results.bed hg19.chrom.sizes blat_results.bb

5. Build a track hub from your bigBed file following the steps at http://http://genome.ucsc.edu/goldenPath/help/hubQuickStart.html
6. In your publication, provide a link that loads your track hub in the UCSC Genome Browser (e.g., http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt). More information on building a link like this is available in the Track Hub User Guide at http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Session.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

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