help with the View, DNA function
Michela Barbaro
Hi,
I use quite a lot the function from the genomebrower to download a DNA sequence of my interest through the View/DNA function
I use the advanced option "extended color case/color option"
Lately I'm experiencing problem when I want to "colour" the track "All SNPs(150)": I do not get any sequence, just an empty page.
While if I select to colour any other SNPs track such as "Common SNP(150) or "All SNPs(147) I get the a nice colored DNa sequence.
This problem occours every 5 or 6 sequences I try t odownload.
How can it be solved? What can it be?
Thanks for your help,
MIchela
Michela Barbaro
PhD, hospital Chemist
Karolinska University Hospital
17176 STockholm, Sweden
Brian Lee
Dear Michela,
Thank you for using the UCSC Genome Browser and your question about the issue when using snp150 and the extended color option for getting DNA.
Could you share an example region?
From speculation about a related mailing list question involving snp150, I believe what is happening is that the vast number of increased SNP annotations in snp150 is leading to a Browser timeout. Here is an example session where you can quickly see visually the increase in annotations in snp150 versus snp147 (on the bottom):
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg38.snp147.150
Across the genome the snp150 table has about 234 million entries while snp147 has about 158 million. This means that in every region, such as in the above session, there will be about 50% more SNPs in snp150 and a consequential delay to process complicated queries such as Table Browser intersections, or selecting and coloring of bases.
One imperfect solution would be to create temporary custom tracks of the region you are interested in annotating. By going to the Table Browser with the snp150 table selected (group: Variation table: All SNPs snp150) you can set the output to "custom track" and then get a small custom track in the Genome Browser annotating the SNPS in your current view (be sure to click the "region:" button next to "position" and not "genome" and then "get output"). Then when you go back to View DNA (there is a keyboard shortcut "v d" to jump to this screen) and get the extended options you could use that Table Browser created custom track (with a name like tb_snp150) to do the processing for your region. Again if you still have many many SNPS in the region you are viewing it might not speed the process up. Also it could be that you have discovered a different issue, so please do respond with more information (for example if there is no response in a region with few SNPs that might be surprising).
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
Brian Lee
UCSC Genomics Institute
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