[genome] In table browser, when I select the genome option in 'region', the analysis accuses time-out

[Cristina Ferreira]

Dear UCSC Genome Browser support team, 

Brian, thank you very much for your explanation in my previous doubt. Now I got the SNPs, as I wish! In the meantime, I'm going to use of the example Genes list you provided to introd

uce another problem I've been seeing. ---- Test you asked me to perform ---- Going to the Table Browser make the following selections: group: Genes and Gene Predictions track: UCSC Genes table: knownCanonical (instead of the default knownGene) region: genome identifiers: Click "paste list" and paste something like the below: IL9R TNF IRF6 IL2 IL6 IL9 IL10 IFNG CSF2 RELA NFKB1 Change "output format:" to "custom track" and "get output" and then "get custom track in table browser." Now you can follow the steps you were doing before: group: Variation track: All SNPs (150) table: snp150 region: genome (This is the point of my doubt)

intersection: Custom tracks -> My gene custom -> I choose: '... any overlap ...' and click "submit" When I use a set of genes from different chromosomes, for intersection with allSNPs on table browser, for example, I need to select each chromosome, of which my genes are represented. Because when I select the genome option in 'region', and I ask for the custom track, the browser accuses time-out.

I used the set of genes that had suggested to me, in the previous doubt (only 11 genes in different chromosomes). List Presented above.

I am sending some examples of screenshot showing the time-out, when I try the genome option, the IL9R (ChrX), with the custom track obtained after selecting ChrX in 'region' option, and the absence of custom track for the TNF gene ( Chr6), since it was necessary to select ChrX and the genome option does not allow access to all data for intersection.

The selection of specific Chr has been necessary, regardless of the amount of genes / physical positions I am using in my gene pool.

Is there any way I can re-select the genome option in the table browser?

Best regards

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Cristina Ferreira

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[Brian Lee]

Dear Cristina,

Thank you for your nice message and for correcting me. In the example I shared I was using the UCSC Genome Browser snp150Common table which has 14 million entries and is about 16 times smaller than the snp150 table, which has 234 million entries.

You are absolutely correct that you should rather limit the regions for each of your sections, avoiding using "region: genome" for the snp150 table, and instead selecting each chromosome to get your output. As you discovered, when the Table Browser attempts to do the intersection across the genome and the 234 million entries in the snp150 it will likely timeout.

There is another option if you were interested in fast responses and not using the Table Browser by downloading the table file and doing a command-line extraction of information. For example, see this previously answered question for snp147, where the BED file of coordinates like the one used in the previous answer is in a file called myCoordinates.txt and one can extract those SNPS quickly with a command like: zcat snp147.txt.gz | grep -Fwf myCoordinates.txt > mySnps.txt

https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/zSKK9e0aVEs/pLM2wBrCBAAJ
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/wPh0J3fadNg/1_x9Eqtg9TYJ

Thank you again for helping point this issue for any future readers who look at our archived mailing list and for 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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