download transcript TPMs?

[Federico Nichetti]

Hi there,

how can I download transcript specific TPMs from https://xenabrowser.net/transcripts/ ?

I am interested in getting FGFR2b (ENST00000457416.6) TPMs from  TCGA STAD.

Thanks in advance

[Mary Goldman]

Hi Federico,

The Transcript Browser is designed to compare one group of donor samples to another group of donor samples (e.g. normal stomach tissue from GTEx donors to tumor tissue from TCGA donors).

It sounds instead like you want to download this data. I created a bookmark with the data I believe that you are interested in here: https://xenabrowser.net/heatmap/?bookmark=3dcc9db26bef3a8dd8a06dceae0de5e5 . Note that there are 2 columns for ENST00000457416.6, one for TPMs estimated by the Kallisto algorithm (column D) and one for TPMs estimated by the RSEM algorithm (column E). To learn more about the data in a column click the 3 dot menu at the top of the column and choose 'About'.

To download the data, click the download icon at the top upper left corner next to the PDF and help icons. This will download a TSV of the data on the screen.

If you would like to investigate other isoforms, hover between columns and then click to add a new column. Enter your transcript and then choose 'Advanced'. Scroll until you see the transcript-level datasets and choose whichever ones you are interested in. Note that this dataset uses transcript IDs from Gencode v23.

If you have any questions, please let me know.

Best,

Mary

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Mary Goldman (she/her), Design and Outreach Engineer 

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

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