how to do gene annotation
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Entering edit mode
6.6 years ago
mms140130 ▴ 60

Hello I have the following data about copy number variation for breast cancer (BRCA) and I want to do gene annotation according to the start , end locations, I downloaded the data from firebrowse

here is part of the data

Sample  Chromosome  Start   End Num_Probes  Segment_Mean
TCGA-3C-AAAU-10A-01D-A41E-01    1   3218610 95674710    53225   0.0055
TCGA-3C-AAAU-10A-01D-A41E-01    1   95676511    95676518    2   -1.6636
TCGA-3C-AAAU-10A-01D-A41E-01    1   95680124    167057183   24886   0.0053
TCGA-3C-AAAU-10A-01D-A41E-01    1   167057495   167059336   3   -1.0999
TCGA-3C-AAAU-10A-01D-A41E-01    1   167059760   181602002   9213    -8.00E-04
TCGA-3C-AAAU-10A-01D-A41E-01    1   181603120   181609567   6   -1.2009
TCGA-3C-AAAU-10A-01D-A41E-01    1   181610685   201473647   12002   0.0055
TCGA-3C-AAAU-10A-01D-A41E-01    1   201474400   201474544   2   -1.4235
TCGA-3C-AAAU-10A-01D-A41E-01    1   201475220   247813706   29781   -4.00E-04
TCGA-3C-AAAU-10A-01D-A41E-01    2   484222  51515129    30300   0.0044
TCGA-3C-AAAU-10A-01D-A41E-01    2   51517041    51524666    11  -1.1753
gene R • 1.6k views
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3
Entering edit mode
6.6 years ago
Samuel Brady ▴ 330

You can download gene/transcript locations from UCSC here:

hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz

That link is for the hg19 version of the human genome. I'm not sure which build is used in the TCGA file you have, but just make sure that the refGene.txt file you get from UCSC matched the genome build in your TCGA copy number file.

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