Question: Query UCSC Browser
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gravatar for FGV
11 months ago by
FGV110
FGV110 wrote:

Dear all,

I'm trying to query the UCSC database directly from the command line (or R) to get the conservation (e.g. phastCons46wayPrimates) score for a single position. I tried using the Table Browser, and it worked fine:

track type=wiggle_0 name="Primate Cons" description="Primate Conservation by PhastCons"
#   output date: 2018-08-07 09:39:08 UTC
#   chrom specified: chr21
#   position specified: 33036558-33036607
#   This data has been compressed with a minor loss in resolution.
#   (Worst case: 0.00497656)  The original source data
#   (before querying and compression) is available at 
#       http://hgdownload.cse.ucsc.edu/downloads.html
variableStep chrom=chr21 span=1
33036558    0.0501575
33036559    0.0451417
33036560    0.0451417
33036561    0.0351102
33036562    0.0451417
33036563    0.0501575
33036564    0.0652047
33036565    0.0702205
33036566    0.0952992
33036567    0.115362
33036568    0.125394
33036569    0.130409
[...]

I then tried several approaches from the command line, but none worked.

Heng Li's script:

echo "chr21 33036558 33036607" | perl batchUCSC.pl -d hg19 -p 'phastCons46wayPrimates:chromStart:chromEnd:*'

Direct mySQL query:

mysql hg19 --user=genome --host=genome-mysql.cse.ucsc.edu -A -NBe 'select * from phastCons46wayPrimates where chrom = "chr21"'

It seems that only some positions are present. Can it be? Is it possible to get per-positions conservation? thanks,

ucsc api • 204 views
ADD COMMENTlink written 11 months ago by FGV110
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