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