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BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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STAR Counts error #500

Open Sandyyy123 opened 2 years ago

Sandyyy123 commented 2 years ago

Hi, I ran this command 2 weeks ago, it ran perfectly.

query = GDCquery(project = 'TCGA-LUAD', data.category = 'Transcriptome Profiling', data.type = 'Gene Expression Quantification', experimental.strategy = 'RNA-Seq', workflow.type = 'HTSeq - FPKM-UQ')

GDCquery(project = "TCGA-LUAD", data.category = "Transcriptome Profiling", : Please set a valid workflow.type argument from the list below: => STAR - Counts

Even, after changing the workflow.type to 'STAR - Counts', I land up with errors in subsequent steps when preparing the dataset using GDCprepare

I updated TCGA biolinks and the compatiable TCGAbiolinksGUI.data packages (=>1.15 version), but the problem did not resolve.

install.packages("https://bioconductor.org/packages/devel/data/experiment/src/contrib/TCGAbiolinksGUI.data_1.15.1.tar.gz",repos=NULL, type="source", build=FALSE)

BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")

ShixiangWang commented 2 years ago

Check https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/493 may help.