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Recovering datasets metadata from the GDC portal

In this first phase, we are going to select the datasets we want to download, and create a file containing dataset metadata that will be required later for downloading the data.

1. Connect to the GDC portal

2. Click the Project button

   

   The project table then displays 64 projects at the date February 19, 2020

   You can restrict the project list using the selectors in the left hand vertical bar:

   Click the TARGETcheckbox → Only 9 projects are left in the table, including the TARGET-AML one. Click on it !

   

3. File Selection

   In this use case, we are interested in RNAseq files. The GDC portal is a rich interface and there is several ways, all valuable, to reach the same selection level. Here is a way:

   • In the section Cases and File Counts by Experimental Strategy click the link in the column Files and the row RNA-Seq that is 778 at the date of February 19, 2020
   • In the file list that is displayed, you can now see that some files are accessible (open), whereas others are not (controlled)
   • Click the checkbox open at the bottom of the left selectors bar.
   • Further restrict the file list by checking the checkbox HTSeq - FPKM
   • You should have now ~187 files selected, out of which 20 are displayed
   • Click on the upper cart icon, the one that contains a menu arrow

   

   • → Add all files to the Cart
   • A green window will prompt that 187 files have been added to the cart and the main top menu should display this:

   

4. File metadata recovery

   • Click on the Cart icon in the main upper menu
   • Click on the Sample Sheeticon

   

   • This will trigger the download of a file whose name is in the form of gdc_sample_sheet.yyyy-mm-dd.tsv and the content looks like:

     File ID File Name   Data Category   Data Type   Project ID  Case ID Sample ID   Sample Type
     0d3ddab0-4c6e-4f96-88dc-3c9813d9c292    2a3814fb-e9b1-404c-95da-db348ecfa14a.FPKM.txt.gz    Transcriptome Profiling Gene Expression Quantification  TARGET-AML  TARGET-20-PAEFGT    TARGET-20-PAEFGT-03A    Primary Blood Derived Cancer - Peripheral Blood
     cc802aa8-e299-40c3-9539-a854ef950ff6    6f475a4d-53ea-4110-b80f-d519289d41f9.FPKM.txt.gz    Transcriptome Profiling Gene Expression Quantification  TARGET-AML  TARGET-20-PASMHY    TARGET-20-PASMHY-03A    Primary Blood Derived Cancer - Peripheral Blood
     85310996-75c9-4b5b-a16e-406cde0a3373    7d07636d-e4cb-4642-83ee-c04b21d15227.FPKM.txt.gz    Transcriptome Profiling Gene Expression Quantification  TARGET-AML  TARGET-20-PASWAJ    TARGET-20-PASWAJ-04A    Recurrent Blood Derived Cancer - Bone Marrow
     0dc459fe-ac56-42af-9c99-3fe3e14bc156    a405cab4-28d0-4cf3-b3c0-2007539002f3.FPKM.txt.gz    Transcriptome Profiling Gene Expression Quantification  TARGET-AML  TARGET-20-PAMVKZ    TARGET-20-PAMVKZ-09A    Primary Blood Derived Cancer - Bone Marrow
     e8a0e021-96cd-4ced-b881-da6b31351ac3    a9fd9d1c-348f-41a9-9da2-a72981ef1ae5.FPKM.txt.gz    Transcriptome Profiling Gene Expression Quantification  TARGET-AML  TARGET-20-PANFMG    TARGET-20-PANFMG-09A    Primary Blood Derived Cancer - Bone Marrow
     5b28c25d-8775-403d-b286-dc88fa3a2d17    bd29f662-4f53-43ce-ad0f-ebcb62546109.FPKM.txt.gz    Transcriptome Profiling Gene Expression Quantification  TARGET-AML  TARGET-20-PAMYGX    TARGET-20-PAMYGX-09A    Primary Blood Derived Cancer - Bone Marrow
     23735039-36e9-4029-bb57-e2ccab9598ed    f49764c5-6b18-435a-90de-64f114a4ce89.FPKM.txt.gz    Transcriptome Profiling Gene Expression Quantification  TARGET-AML  TARGET-20-PASVVS    TARGET-20-PASVVS-04A    Recurrent Blood Derived Cancer - Bone Marrow
     30a6e42d-81de-4837-abb4-84a3687f60de    2f601196-beaf-4a1e-91ee-72ef1de17f98.FPKM.txt.gz    Transcriptome Profiling Gene Expression Quantification  TARGET-AML  TARGET-20-PANHYK    TARGET-20-PANHYK-09A    Primary Blood Derived Cancer - Bone Marrow
     6694923c-6ac6-4ba8-bddc-b35f438924b9    50b79e4d-0e67-4d79-914f-924e0ea920d9.FPKM.txt.gz    Transcriptome Profiling Gene Expression Quantification  TARGET-AML  TARGET-20-PAPWYK    TARGET-20-PAPWYK-09A    Primary Blood Derived Cancer - Bone Marrow
     a0f31602-503b-4964-b68c-1ef996536a74    b5514b40-5b8b-4faf-a202-49438c386032.FPKM.txt.gz    Transcriptome Profiling Gene Expression Quantification  TARGET-AML  TARGET-20-PARGVC    TARGET-20-PARGVC-03A    Primary Blood Derived Cancer - Peripheral Blood
     

     Here we are ! In the next section, we will manipulate this metadata file, in order to use it for batch downloading of the data files