failed to open file using Signac maybe related to Rsamstools
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Haemin • 0
@bfad447f
Last seen 2.7 years ago
South Korea

Hi, I'm trying to learn scRNA-seq and ATAC-seq integrated analysis using Vignettes produced by Satija lab. And I'm stucked in "quantify gene activity" step due to the inability to run the code below.

gene.activities <- GeneActivity(pbmc.atac, features = VariableFeatures(pbmc.rna))

it returns

Extracting gene coordinates
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'y' in selecting a method for function 'intersect': failed to open file: https://cf.10xgenomics.com/samples/cell-arc/1.0.0/pbmc_granulocyte_sorted_10k/pbmc_granulocyte_sorted_10k_atac_fragments.tsv.gz

I found the other guy having same problem in the github and it seems he/she didn't get the solution from Signac developer, issuing it's not the problem of Signac package. https://github.com/satijalab/seurat/issues/4402

Can anyone solve the problem? or have any other option to bypass the failure of tbx file loading?

Rsamtools • 965 views
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