Downloading controlled access data from ICGC for specific ID?
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5.0 years ago
ivivek_ngs ★ 5.1k

I remember there are only few posts regarding the controlled access data download from ICGC and so I am trying to ask a specific question with regards to the same.

  1. I am having controlled data access for ICGC and I have generated the required tokens that are needed for downloading the data from specific mirrors. Now what I understand from their GUIDE is that it is pretty straight forward to download the various mutation or count files, however, there is no documentation for downloading the .bam files from any of the specific mirrors. I might have missed it as well but if kindly someone can point out.
  2. Another problem is can't we download specific bam files if we provide the DONOR ID which is usually unique or specific ID that is unique for a study ? I have not found any document for such as well.
  3. Does anyone have experience in downloading only RNA-Seq bam files for specific studies like OV-AU providing specific DONOR ID? If so can you point me out to a documentation from where you did that? I have already installed the client (get and storage) but cannot proceed with the bam files download. There is no mention of bam file download there. Probably I am missing some documentation. If anyone has the experience of such downloads kindly share.

If this question is too broad for the forum kindly close it or if you need any more information please feel free to ask, if the moderator thinks. Thanks a lot

icgc RNA-Seq • 1.2k views

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