CPTAC-3 GDCPrepare with scRNA-seq data

[LeaLe88]

Good afternoon,

I am having issues with GDCPrepare with the CPTAC-3 dataset for scRNA-seq data.

I have successfully downloaded the data with

#Query the data
   query.exp <- GDCquery(
       project = "CPTAC-3",
       data.category = "Transcriptome Profiling",
       experimental.strategy = "scRNA-Seq",
        workflow.type="CellRanger - 10x Filtered Counts",
        data.type = "Gene Expression Quantification",
        sample.type = c("Primary Tumor")
   )

#Get results
output.query<-getResults(query.exp)

#Downloads the data
 
#GDCDownload(query.exp)
   GDCdownload(
       query = query.exp,
       files.per.chunk = 100
   )
 

However, it is giving me the following error when trying to use GDCPrepare with GDCprepare(query.exp) :

t::Read10X(data.dir = gsub("\\.tar\\.gz", "", f)) : 
  Directory provided does not exist
Error in if (value == n) { : argument is of length zero

Do you have any idea what could be the issue? Maybe for scRNA seq I cant use the summarized Experiment?

Thanks a lot,
Lea

[LeaLe88]

Good morning,

Has anyone an idea on this?

Thanks a lot,
Lea