Here we will use the 1k PBMCs from a Healthy Donor (v3 chemistry) from 10x genomics, consisting of 1000 Peripheral blood mononuclear cells (PBMCs) extracted from a healthy donor, where PBMCs are primary cells with relatively small amounts of RNA (~1pg RNA/cell). The second part of this tutorial also has a one-click solution to producing a matrix identical to that given by the Cell Ranger pipeline, but the more interesting aspects of the pipeline are explored in the Introspective Method part of the tutorial. Notice the order of magnitude speed up that STARsolo and a few others display, for a variety of different datasets in comparison to Cell Ranger. Since STARsolo is a drop-in solution to the Cell Ranger pipeline, the first part of the tutorial is a one-click solution where users are encouraged to launch their RNA STARsolo jobs and spend the time familiarising themselves with the pre-processing training materials mentioned above.ĭetails: Benchmark of Cell Ranger to others Figure 4: Benchmark of different mapping software. However, those who are more interested in learning the intricacies of how FASTQ files are transformed into a count matrix, please see the Pre-processing of Single-Cell RNA Data tutorial.ġ0x Genomics has its own processing pipeline, Cell Ranger to process the scRNA-seq outputs it produces, but this process requires much configuration to run and is significantly slower than other mappers. The first part of this tutorial is essentially a one-click “fire and forget” solution to demultiplexing and quantifying scRNA-seq data, where much of the complexity required in this extremely crucial stage is simplified into a single step.
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