Getting started with Arabidopsis thaliana genomics

I have started to work on Arabidopsis thaliana, as I mentioned in my last post. As noted in the Encyclopedia of life: Arabidopsis thaliana is the most widely used model organism in plant biology. Its small genome size, fully sequenced in the year 2000, chromosome number, fast growth cycle (from seed germination to set in...

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Read GTF file into R

The Gene Transfer Format (GTF) is a refinement of the General Feature Format (GFF). A GFF file has nine columns: seqname The name of the sequence; must be a chromosome or scaffold. source The program that generated this feature. feature The name of this type of feature, e.g. "CDS", "start_codon", "stop_codon", and "exon" start The...

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Getting started with Seurat

This post follows the Peripheral Blood Mononuclear Cells (PBMCs) tutorial for 2,700 single cells. It was written while I was going through the tutorial and contains my notes. The dataset for this tutorial can be downloaded from the 10X Genomics dataset page but it is also hosted on Amazon (see below). The PBMCs, which are...

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Learning about Snakemake

As promised two years ago, here's a short blog post on Snakemake. I have been using Bpipe to manage my workflows/pipelines but Snakemake has been mentioned to me on more than one occasion; in particular: @davetang31 seems useful if testing many diff types of pipelines. snakemake seems a bit more practical if analyzing many samples...

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Incidental findings using GEMINI

The American College of Medical Genetics and Genomics (ACMG) have recommended that genetic variants that may be pathogenic or likely pathogenic in certain genes should be reported back to the patient. The latest list of genes can be found here. How do I assess whether a variant is pathogenic or likely pathogenic? Use this tool,...

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Summary plots from GEMINI

I'm a fan of GEMINI and have been using it for for a year and a half for various exome projects. I have written two scripts that can generate variant summaries from a GEMINI database. I prefer bar plots over the pie charts created by VEP. A summary pie chart created by VEP.

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