14 02, 2017

Understanding a 10XGenomics Cell ranger QC report

By | February 14th, 2017|Categories: "Experimental design controls etc", Single-cell sequencing|Tags: , |3 Comments

This post: “Understanding your 10XGenomics cell ranger report” originally appeared on my labs group blog but I thought that people working with single-cell who are at AGBT might like to read it too. Understanding your @10Xgenomics cell ranger reports The 10X Genomics Cell Ranger analysis […]

10 02, 2017

Fingerprinting for multiplexed single-cell RNA-seq

By | February 10th, 2017|Categories: "Experimental design controls etc", "My almost"..., 10X Genomics, Methods and applications, Next-generation sequencing, Single-cell sequencing|Tags: |0 Comments

In this post I describe an idea for using SNP fingerprinting for single-cell RNA-Seq to identify which sample each individual cell comes from in a multiplexed library prep. The reason for my thinking about this is that single-cell experiments are expensive. Although the cost-per-cell can […]

21 12, 2016

Problems for breast cancer researchers in 2017?

By | December 21st, 2016|Categories: "Experimental design controls etc", Other stuff|1 Comment

Breast cancer researchers publish a lot of papers, and a large number of those will include some genomics, variant identification, RNA-Seq, ChIP-Seq, etc. Increasingly research is being carried out on patient derived material, but cell lines are still a vital part of much of the […]

14 10, 2016

Batch effects in scRNA-seq: to E or not to E(RCC spike-in)

By | October 14th, 2016|Categories: "Experimental design controls etc"|0 Comments

At the recent Wellcome Trust conference on Single Cell Genomics (Twitter #scgen16) there was a great talk (her slides are online) from Stephanie Hicks in the @irrizarry group (Department of Biostatistics and Computational Biology at Dana-Farber Cancer Institute). Stephanie was talking about the recent work she’s […]

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