Hello Shawn,

To do this in three steps:

1 - Format your existing file, set type as interval,
    and assign columns ("Edit attributes").

    Start by changing this:
    chr10:11,997,707-12,330,274
    To become like this, separated by tabs:
    chr10  11997707  12330274

    Add in strand if possible:
    chr10  11997707  12330274  +

2 - Obtain a mapped transcript file that includes gene identifiers

    a) Once choice is UCSC's "Known Genes" track:
    From your working history, use tool "Get Data -> UCSC main"
    Select the genome (hg18) and the track "UCSC Genes", with
    output = selected fields from primary and related tools and
    merge in identifiers from tables such as "hg18.kgXref". The
    track "RefSeq Genes" is another option (RefSeq accession is
    "name" and gene identifier is "name2". Send query to Galaxy,
    set type as interval, and assign columns.

    b) Another choice would normally be Ensembl Genes from
    "Get Data -> Biomart", but only hg19 is available.

3 - Merge the files based on overlap

    The tool you will most likely want to use is "Operate on
    Genomic Intervals -> Join", although you may want to
    explore others.

    Help:
    http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
    also see screencasts at http://usegalaxy.org
    quickies #3 & #5 to start with


Hopefully this helps to get you started!

Thanks,
jen

On 7/21/11 4:37 PM, Shawn Anderson wrote:
Hello,

I'm not sure if this is the place to ask this, but if so - here goes. If
I have a list of genomic regions (from CNV gains and losses) comprised
of chromosome, start and stop (ie. chr7 68000000 71000000) for a given
genome build (HG 18), and I want to add the genes (ideally HUGO gene
Symbols or refseqIDs)that reside within each region per line.

So I want to input something like this:

Sample

        

Chromosome Region

        

Event

        

Length

JC 507 CD19

        

chr10:11,997,707-12,330,274

        

CN Gain

        

332568

JC 507 CD19

        

chr10:47,563,503-48,085,608

        

CN Loss

        

522106

JC 507 CD19

        

chr10:69,510,584-69,951,738

        

CN Gain

        

441155

And get an output similar to this:

Sample

        

Chromosome Region

        

Event

        

Length

        

Gene Symbols

JC 507 CD19

        

chr10:11,997,707-12,330,274

        

CN Gain

        

332568

        

CDC123, DHTKD1, NUDT5, SEC61A2, UPF2

JC 507 CD19

        

chr10:47,563,503-48,085,608

        

CN Loss

        

522106

        

AGAP9, ANXA8, ANXA8L1, CTSL1P2, FAM25B, FAM25C, FAM25G, GDF10, GDF2,
LOC642826, RBP3, ZNF488

JC 507 CD19

        

chr10:69,510,584-69,951,738

        

CN Gain

        

441155

        

ATOH7, DNA2, HNRNPH3, MYPN, PBLD, RUFY2, SLC25A16

Possible ?

*Shawn Anderson*

Application Scientist -*Laboratory****for Advanced Genome Analysis*

Vancouver Prostate Centre - Vancouver General Hospital

2660 Oak Street

Vancouver BC V6H 3Z6

P:604-875-4111 ext. 63436

F:604-875-5654

_sander...@prostatecentre.com <mailto:sander...@prostatecentre.com>_

www.LAGAPC.ca <http://www.microarray.prostatecentre.com/>



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