Obtaining the CNA data
1
0
Entering edit mode
2.9 years ago

Hi

I want to obtain the CNA data for particular cancer type. I downloaded the data from Gistic and Cosmic, but I didnot get the data in the form I want. I want the data cancerwise, patientwise and genewise, like we get the expression data.

From Gistic, I downloaded different files as: gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.mage-tab.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.mage-tab.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.Level_4.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.Level_4.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.aux.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.aux.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.mage-tab.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.mage-tab.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.aux.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.aux.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.aux.2016012800.0.0

Please suggest

Regards

Shivangi

cna cancer • 689 views
ADD COMMENT
0
Entering edit mode

Hello shivangi.agarwal800!

What have you tried? Please show us you have invested some effort and I will reopen the question. You can edit your question and add relevant details, then reply to this comment to alert me of the edit.

ADD REPLY
0
Entering edit mode

I downloaded the data from Gistic and Cosmic, but I didnot get the data in the form I want. I want the data cancerwise, patientwise and genewise, like we get the expression data.

From Gistic, I downloaded different files as: gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.mage-tab.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.mage-tab.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.Level_4.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.Level_4.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.aux.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.aux.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.mage-tab.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.mage-tab.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.aux.2016012800.0.0.tar.gz gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.aux.2016012800.0.0.tar.gz.md5 gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.aux.2016012800.0.0

ADD REPLY
0
Entering edit mode

Please edit your question and add this information there.

ADD REPLY
0
Entering edit mode

Have edited the original question

ADD REPLY
0
Entering edit mode

I've reopened your question.

ADD REPLY
0
Entering edit mode
2.9 years ago

Hi

While unzipping TP.CopyNumberLowPass_Gistic2.aux.2016012800.0.0.tar.gz, there is GDAC_Gistic2Report_22529547_broad_data_by_genes.txt file. While looking into the contents, I got as

GDAC_Gistic2Report_22529547_broad_data_by_genes.txt | cut -f-15 Gene Symbol Locus ID Cytoband TCGA-3C-AAAU-01A-11D-A41E-01 TCGA-3C-AALI-01A-11D-A41E-01 TCGA-3C-AALJ-01A-31D-A41E-01 TCGA-3C-AALK-01A-11D-A41E-01 TCGA-4H-AAAK-01A-12D-A41E-01 TCGA-5L-AAT0-01A-12D-A41E-01 TCGA-5L-AAT1-01A-12D-A41E-01 TCGA-5T-A9QA-01A-11D-A41E-01 TCGA-A1-A0SB-01A-11D-A141-01 TCGA-A1-A0SD-01A-11D-A111-01 TCGA-A1-A0SE-01A-11D-A087-01 TCGA-A1-A0SF-01A-11D-A141-01

ACAP3 116983 1p36.33 0.000 -0.518 -0.240 0.000 0.000 0.000 0.000 -0.647 0.000 0.000 0.000 0.322

I did not understand why there are different values (0.00, -0.518, -0.240, 0.000) for different patients when Gene Symbol,Locus ID and Cytoband are same. Can anyone suggest??

Regards

ADD COMMENT
0
Entering edit mode

Hello,

Is this an answer to your top level question?

ADD REPLY

Login before adding your answer.

Traffic: 2609 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6