Posts

• January 29, 2019 Error report: two errors I encountered while running GATK VariantRecalibrator

  I was running GATK’s VariantRecalibrator today with the following command and run into a couple of errors:

• January 6, 2019 Download and align single cell RNA-seq data: Part II

  Here is the code I use to align downloaded RNA-seq datasets.

• December 14, 2018 Download and align single cell RNA-seq data: Part I

  Although post-alignment transcriptomic datasets are readily available, from time to time, one may consider realign the raw reads. The reason for realignment can be 1) to make mapping parameters (especially genome annotations) consistent; 2) adding new analysis that was not part of the original procedure. In any case, it starts from downloading raw data from an online data repository (e.g. GEO) and then align the raw data to a desired genome with appropriate annotation. I will go through the basic processes in this post.

• November 27, 2018 Combining Multiple Single cell RNA-seq Datasets: Part III

  I combined individual expression data files from Fan et al., 2018 study to generate a Seurat project for downstream analysis.

• October 24, 2018 Combining Multiple Single cell RNA-seq Datasets: Part II

  In this post, I will try to combine Nowakowski et al., 2017 , BrainSpan and Zhong et al., 2017 datasets.

• October 21, 2018 Combining Multiple Single cell RNA-seq Datasets: Part I

  Since single cell RNA-seq becomes an affordable and accessible technology to any lab around the world, there have been a lot of datasets generated (for a list of existing datasets, visit the Resource page). The number of cells in these datasets ranges from hundreds to thousnads, to even tens of thousands. To use all of these datasets more efficiently, it is a good idea to combine them.