Question: Identifiers Have No Match In Ucsc Xyz Tables? Any Easier Solution?
0
gravatar for CrazyB
5.3 years ago by
CrazyB210
United States
CrazyB210 wrote:

(newly edited version) I try using UCSC Table Browser to help summarize SNP data, but have encountered the same problem all the time. Wherever and whenever I paste a bunch of SNPs onto UCSC table browsers, I almost always get a warning message from UCSC that says, for example, "Note: 24 of the 1452 given identifiers (e.g. rs77757981) have no match in table snp138, field name. Try the "describe table schema" button for more information about the table and field."

UCSC table browser never "tells me" which identifiers in my list have no match, although they do provide explanations in their "sequence and annotation download section" that certain types of rs# would be excluded from their tables. Theoretically I could download all FASTA files for the snp build and compare my list with them, separate the rs# that do not match before I paste the rest to Table Browser for summary. I was wondering if anyone has a better idea how to find out more easily which rs# would not be matched to UCSC tables.

Great many thanks

identifiers • 1.7k views
ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by CrazyB210
1
gravatar for Pierre Lindenbaum
5.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:
ADD COMMENTlink written 5.3 years ago by Pierre Lindenbaum120k

Thanks a lot for the feedback. Apology for my original question that was poorly phrased (has since been re-phrased). My problem is UCSC does not let me know which rs# are not matched in their table. Although I know I could find out the specific info of each rs# from the links you provided, I need to know first which rs# UCSC could not match.

ADD REPLYlink written 5.3 years ago by CrazyB210

use comm http://linux.die.net/man/1/comm

ADD REPLYlink written 5.3 years ago by Pierre Lindenbaum120k
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