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

_sanderson@prostatecentre.com <mailto:sanderson@prostatecentre.com>_

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

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