Dear CGC team, When I compare the mutation data I download from the TCGA website (maf files), they don't match up with the data displayed in CGC. For example, in ovarian cancer 8% and 9% of patients are BRCA1 and BRCA2 mutated. When I pull these data up in the browser, there are only 2 BRCA2 mutations showing up. The same pattern is true for TCGA LUSC and BLCA, with CGC displaying fewer mutations than shown in the raw data. Can you please explain this discrepancy? Thanks, An

I would like to download the meta-data for a set of files. For examples, I have four gene-wise readcounts text files. Each file has associated metadata: platform type, reference genome, disease, investigation etc. I would like to download the associated metadata for a set of files, as a text file, onto my local machine. Is it possible to do this? Thanks, Anjan

Hi, If I want to run a program on a WES from TCGA-CG-5720 in TCGA STAD, how can I add this one bam file to a Project? Nothing came ot when I typed "TCGA-CG-5720" in search window. Do you have any idea? Thanks, HoJoon

I can view the values in the clinical xml files - but can I use those values to filter a selection or add to analysis? Thanks.

Hi! Which is the best way to get access to the expression of long non-coding RNAs? Is there any processed data (I have already checked on the case explorer) or I should reanalyze the raw data using something like Cufflinks?

I've joined today as a beta user and started a project, but once I do a query and pull up a list of files, I'm unable to highlight them either on the query map or the list of files in order to add them to my project for analysis. Is this a bug or am I doing something wrong? The help page indicates that I should be able to click on a path to highlight and add those files. Thanks!

HI there, I've noticed that some TCGA samples have multiple RNA-Seq BAM files, what would be the difference between the files? If it's convenient to use one over the other, what criteria should be used to select such file. Example: TCGA-STAD RNA-seq TCGA-BR-8368-01A-11R-2343-13_rnaseq.bam 14.5GB _1_TCGA-BR-8368-01A-11R-2343-13_rnaseq.bam 14.7GB Thanks, Franco

I'd like to test some of my tools on this platform. I was wondering if there was any data that's not TCGA-restricted that everyone can access and use, just for getting familiar with the environment. This could perhaps be 1kG data or cell-line data. I guess the alternative is to upload and use private data but I wanted to check what's recommended. Thanks, Avi

Hi! I'm trying to download the diagnosis data to see if I can find some correlations with my gene of interest. In the Data browser I can see the Diagnosis Details but despite making subgroups for the data import I can't get those details in the metadata file. Is there any way to extract them? Thanks

Hi! I used to be able to find my gene of interest (C1ORF61) using the Case Explorer but now I can't find it any more. Is there any gene re-naming in this latest version? Thanks!

I have trouble matching WSI slides to their grade, or TNM. For example, patient: TCGA-BC-A110 has three slide samples: Sample TCGA-BC-A110-01Z (Primary Tumor) Sample TCGA-BC-A110-01A (Primary Tumor) Sample TCGA-BC-A110-11A (Normal tissue) Question 1: Is it correct samples ending with A were all sampled together? Question 2: Can I know which were sampled first? Samples ending with A, or Z? [Pathology report exist only for A, with conclusion of Grade I. Clinical file nationwidechildrens.org_clinical.TCGA-BC-A110.xml states patient had cancer with grade I, and later a reoccurence. It means A is the first tumor event, and Z the second?] Question 3: I noticed pathology reports are never available for Z samples, and only for A. Is there a reason?

I got the HER2, ER, PR status of BRCA patients from the BRCA TCGA publication supplementary: https://www.nature.com/articles/nature11412#supplementary-information filename: TCGA_Supplementary Tables 1-4.csv column: HER2_Final_Status But since it is from 2012, after some months, I downloaded the newer clinical data from cbioportal**: http://www.cbioportal.org/study?id=brca_tcga#clinical filename: data_bcr_clinical_data_patient.txt columns: IHC-Status, HER2 fish status However, I noticed that hundreds patients had different her2 status then they had in the old tcga publication: Barcode IHC-status(cbioportal) Her2 fish status (cbioportal) HER2_Final_Status(tcga publication) TCGA-A1-A0SH Equivocal Negative Negative TCGA-A2-A04U Negative Positive Negative TCGA-A2-A0T2 Negative Not Evaluated Negative TCGA-A8-A06R Positive Positive Equivocal At first, I thought there is a method to convert both ihc and fish statuses into one (final status). But I failed to find such method. In TCGA-A1-A0SH, it seems Fish is prefered. In TCGA-A2-A04U , it seems it is IHC. in TCGA-A8-A06R it is neither. **I verified that for those 4 patients, her2 status is consistent between cbioportal and current TCGA clinical files. (her2_fish_status, her2_status_by_ihc in clinical files) Thanks in advance, Maor

I have download TCGA COAD expression data file which have data like shown below. How these values are calculated and what does means by these values. Hybridization REF TCGA-AA-A00E-01A-01R-A002-07 Composite Element REF log2 lowess normalized (cy5/cy3) collapsed by gene symbol ELMO2 -0.201 CREB3L1 2.3005 RPS11 -0.080375 PNMA1 -1.23175