Where can I find the library type (poly-A or ribo-depleted) for each RNA-seq sample/study in TCGA? I have tried looking through various papers and GDC portal and couldn't find an exact answer.
+1 for this. Maybe downloading metadata using TCGABiolinks and searching for "TotalRNASeqV2" might yield some results - I will try it later and let you know.
Any luck, Barry?
Nothing, unfortunately. GDCquery() only uses 'Illumina' for the platform argument, despite the man pages describing a wide array of options. I double-checked and downloaded all GDCqueries for each project beginning with TCGA and yep, Illumina is the only level in the platform column.
Attempting to filter by experimental.strategy = "Total RNA-Seq" returns NULL objects for all 'TCGA-' projects too.
experimental.strategy = "Total RNA-Seq"
In short, I don't think TCGAbiolinks is a valid option
Perhaps ask the TCGA / GDC directly, @komal.rathi
If you add a custom filter in GDC portal of read_group.library_selection, you will see
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