IGV download visualized data TCGA

[Elena]

Hello,

I loaded CNV data from the TCGA server. Presumably these data are segmented data that have been run through GISTIC already. How can I download the data that IGV is displaying? Is there an export function? It is not found in the publication because TCGA on breast cancer was published in 2012, whereas the dat that IGV is loading is from the servers that have been updated to the newest release in 2016. I understand that I can run GISTIC on this newest segmented data myself but if IGV is displaying it then it must have this data analyzed by GISTIC already. How can I access it?

Thank you,

Elena

[Jim Robinson]

We are not a TCGA download center,  you can't download data from us only view it.  You should be able to find the CNV  data in IGV from here:  https://gdac.broadinstitute.org/.  If you can't find it there use the "Contact Us" button on that webpage.   For other data and more information visit the TCGA website.

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[Elena]

Right, but IGV is displaying not the segmented data but the GISTIC analyzed segmented data. Is that true? That is not available on the TCGA website. 

[Jim Robinson]

Exactly which dataset are you referring to, and which genome assembly?

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[Elena]

You are right IGV is displaying just the segmented data. The difference that I observed is due to TCGA portal providing data for download hg38 but IGV is pulling it from TCGA archives which are hg19 and showing 1 aliquot per patient only. However, I still don't understand why IGV is colouring certain regions grey regardless of whether they are in the segmented data file or not. How does it know what to colour grey, which I am guessing refers to data quality? For example, the region between first rows for chr4 is greyed out chr4:8,104,173-8,104,838 because there is no data for it, which makes sense but why are these rows greyed out?

TCGA-A2-A0CM-01A-31D-A036-01 4 17491913 17492073 2 -2.0284 

TCGA-A2-A0CM-01A-31D-A036-01 4 17492145 53894516 18664 -0.1758 

[James Robinson]

Hi,

Please provide more details when asking questions,  I do not work on TCGA and do not know what you are referring to.   Tell me what menu items to select to load the data you are referring to.

Thanks

Jim

On Aug 4, 2016, at 11:53 AM, Elena <kuzmin...@gmail.com> wrote:

You are right IGV is displaying just the segmented data. The difference that I observed is due to TCGA portal providing data for download hg38 but IGV is pulling it from TCGA archives which are hg19 and showing 1 aliquot per patient only. However, I still don't understand why IGV is colouring certain regions grey regardless of whether they are in the segmented data file or not. How does it know what to colour grey, which I am guessing refers to data quality? For example, the region between first rows for chr4 is greyed out chr4:8,104,173-8,104,838 because there is no data for it, which makes sense but why are these rows greyed out?

TCGA-A2-A0CM-01A-31D-A036-01 4 17491913 17492073 2 -2.0284 

TCGA-A2-A0CM-01A-31D-A036-01 4 17492145 53894516 18664 -0.1758 

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[Elena]

segmented file: http://firebrowse.org/?cohort=BRCA&download_dialog=true --> wait for the pop up window to show up --> then select this file: genome_wide_snp_6-segmented_scna_minus_germline_cnv_hg19  (MD5)

IGV: File --> Load from Server --> The Cancer Genome Atlas --> TCGA Broad GDAC --> Firehose standard data -->  Broad Firehose Standard Data Run: 2016_01_28 --> BRCA-TP --> CopyNumber: [genome_wide_broad_minus_germline]

[James Robinson]

Hi,

There are a two issues here.

First,  gray indicates the absence of data (no segment).     This is normal. 

Second,  I found a bug that in some circumstances would result in a segment not being painted when it should,  specifically if you are zoomed in and the segment starts just to the left of the edge.  I pushed a fix for that and it will be released this evening as version 2.3.80.

Jim

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