Table snp146Common download not complete

[Boel Brynedal]

Hi,

I am using the Table browser to download BED files for SNPs (snp146Common) by uploading a list of identifiers. I am submitting rather long list of identifiers (2.5 million) and this seems to be working OK, and the download concludes without any errors. But the resulting file lacks a couple of identifiers and the last row is not finished. As:

$ tail -n 3 /Users/Boel/Downloads/meta_snps_aa.bed

chr22 50620689 50620690 rs3091400 0 -

chr22 50622239 50622240 rs9628229 0 +

chr22 50622770 50622771 rs$

It is only the last < 100 identifiers that are missing and the problem remains if I ask for ~1 million identifiers. Can one not ask for a large number of identifiers, and what is the upper limit in that case? Querying for ~30 SNPs did not cause any issues. 

I am using the european mirror in Chrome. 

Thanks,

Bo

[Christopher Lee]

Hi Bo,

Thank you for your question about querying the Table Browser. Unfortunately 1 million
identifiers is too many ID's to query the Table Browser with. We suggest halving the number
of ID's per query until you find an acceptable number, as we do not set any hard limits on
the number of ID's since it may vary wildly between different tables.

As an alternative to this binary search method, you can try downloading the table dump for the
snp146 Common table:
http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/snp146Common.txt.gz

and using the following command:
zgrep -Fwf fileOfRsIDs.txt snp146Common.txt.gz

to extract all the lines from the table containing your identifier.

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.

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