Question about ERCC genes in Ziegenhain dataset

bvieth / scRNA-seq-pipelines

Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"

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Question about ERCC genes in Ziegenhain dataset #2

Closed xuebaliang closed 4 years ago

xuebaliang commented 4 years ago

Hello, I have some trouble in finding the ERCC files of Ziegenhain dataset in paper <Comparative analysis of single-cell RNA sequencing methods>. It is likely not on GSE75790 in NCBI . Therefore can you send me it? I want to know the true concentration level of those ERCC genes. Another question is that whether you know the cell types(clusters) for these 583 cells. Thanks.

bvieth commented 4 years ago

Hello,

my apologies for answering so late. I turned off the github notifications since my email would have gotten flooded otherwise.

So concerning your question you can actually find the concentration tables and count matrices for the SCRBseq and Smartseq2 prepared cells in the folder simulation/ saved as rds files. There are no different cell types since they are all mouse embryonic stem cells.

Kind regards Beate