Some questions about using CSeQTL

[zhangpicb]

Dear @sunway1999 @pllittle @liusi2019

Thanks for your beautiful codes and the CSeQTL paper!

I want to run some example data to make sure that I can use CSeQTL correctly.(PS. our lab own CMC and GTEx data)
And I don't find Brain cell type deconvolution signature data.It would be appreciated if the signature data could be shared.(maybe .rData or .RDS file)
I want to use CSeQTL to find cell type specific eQTL in my data.And I don't know how to get residual TReC PCs.

Best,
zhang

[sunway1999]

Hi, zhang, thanks for your interest in using CSeQTL. I have added the exact file name in the README file in the deconvolution section. here is the link: https://github.com/Sun-lab/scRNAseq_pipelines/blob/master/MTG/signature_MTG.rds

[zhangpicb]

Dear @sunway1999 @pllittle

Thanks for your reply!

CSeQTLworkflow/README.md

Line 443 in df7e852

* cell sizes

CSeQTLworkflow/README.md

Line 503 in df7e852

yy = xx / cell_sizes; yy / sum(yy)

I don't find Brain cell size data.
It would be appreciated if the Brain cell size information could be shared.

Thanks in advanced!

Best,
zhang