RE: SCALE

[Jiang, Yuchao]

Hi Mikhail,

Thanks for your interest and your inquiry. Unfortunately, I don't think SCALE would apply to 10X Genomics data. The reason is not the lack of ERCC spike-ins but rather the low depth of coverage and more importantly, the lack of heterozygous SNPs in the 5' end.

Cheers,
Yuchao

-----Original Message-----
From: Olferiev, Mikhail MD <Olfe...@HSS.EDU>
Sent: Wednesday, August 21, 2019 2:50 PM
To: Jiang, Yuchao <yuc...@email.unc.edu>
Subject: SCALE

Dear Yuchai,

My name is Mikhail Olferiev and I am research associate at Hospital for Special Surgery, NY. I was reading your publication SCALE: modeling allele-specific gene expression by single-cell RNA sequencing. It is a great publication and very unique tool.

I wondering is it possible to use SCALE together with 10X genomics scRNA-seq data? The current data do not have ERCC spike, but I plan to implement ERCC in my feature work.

My second question. Could I use phased genome data to improve ASE analysis with scale?

Thank you,

Mikhail Olferiev.