getting snp and restriction Enzyme site from ucsc genome browswer
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Entering edit mode
prabin.dm • 0
@prabindm-9986
Last seen 5 months ago
United States

I am using rtracklayer package to access rs ID and restriction enzyme sites in a genomic interval so that I can make genotyping decisions.

library(rtracklayer)
session <- browserSession()
genome(session) <- "mm9"
trackNames(session) ## list the track names
# for Restr Enzymes use "cutters"

query <- ucscTableQuery(session,"cutters" ,
                        GRangesForUCSCGenome("mm9", "chr7",
                                             IRanges(149627713, 149630315 )))

This yeilds a mesage saying Error in normArgTrack(track, trackids) : Unknown track: cutters

I read that "Note that not all tables are available as tracks.". So I am guessing "cutters" are available as a table but not as a tack. So how to I know which track to query so that I can get cutter table.

rtracklayer • 326 views
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Entering edit mode
@michael-lawrence-3846
Last seen 9 months ago
United States

The table name is "cutters", so you would need to pass that as the table= argument, leaving track=NULL so that it searches all tracks. But in this case UCSC does not provide that table anyway. You can get it from REBASE.

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