24 04, 2017

Update on @illumina index-swapping: better barcode design

By | April 24th, 2017|Categories: "Experimental design controls etc", Core facilities, Methods and applications, Next-generation sequencing|Tags: , , |2 Comments

Last week I followed up on the index-swapping issue after Illumina released their white paper and also covered what Ethan Linck at The Molecular Ecologist had posted about the Sinha et al BioRxiv paper. In that post I said I’d write a follow-up post about index design over the weekend – here it is! […]

21 04, 2017

Update on @illumina index-swapping

By | April 21st, 2017|Categories: "Experimental design controls etc", Core facilities, Design, Methods and applications, Next-generation sequencing|0 Comments

Illumina released a white paper this week describing their efforts to understand the index-swapping issues with the ExAmp chemistry. This story has been covered many times and got lots of Tweets in the days since the BioRxiv paper from Stanford was uploaded. Megan Molteni at Wired wrote a lengthy […]

22 03, 2017

10X Genomics 10x cheaper…and better too!

By | March 22nd, 2017|Categories: "Experimental design controls etc", 10X Genomics, Methods and applications, Next-generation sequencing, Single-cell sequencing, Uncategorized|0 Comments

Confession: this post may not actually make your 10X Genomics experiments ten times cheaper…but implement Demuxlet in your workflow and with the right sort of experiment you might just get there! Single-cell RNA-Seq might just have got a whole lot cheaper, thanks to a method […]

14 02, 2017

Understanding a 10XGenomics Cell ranger QC report

By | February 14th, 2017|Categories: "Experimental design controls etc", Single-cell sequencing|Tags: , |5 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 […]

Load More Posts