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/>



___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to