Thorough guide for optimizing Augustus on well-suited BUSCO genes.
A useful script for identifying the footprints of RAD-seq loci from read mappings
A thorough tutorial on performing whole genome alignment with the Lastz/MultiZ pipeline
Notes for how I configured CPAN on Harvard Odyssey cluster
Notes from a quick introduction session I attended on msprime
How to remove the annoying space in the default Box Sync folder
How to re-establish ZotFile links to PDF attachments
Experimental design activity to accompany an introductory lesson on RAD-seq
How-to guide on quickly determining whether RNA-seq data is stranded
Invited to present work as part of comparative genomics session joint meeting of VGP and EBP.
Genome provides insight into reptilian microchomosomes, venom gene regulation, and sex chromosome evolution.
Accomplished a lot and had some fun in Australia!
How-to on imbedding Gist content into Minimal Mistakes markdown blog post.
Creating a UCSC Genome Track for Viewing Genome Annotations
I have arrived ‘down under’ to begin postdoc research.
Extracting conserved regions sequences from PhastCons conservation tracks.
Notes from work installing and running Provean to predict protein impact of variants.
Installing, authenticating, and downloading using BaseSpace CLI.
Our paper on rapid adaptation in invasive Burmese pythons published in Molecular Ecology!
Details on acquiring reads from BAM file
Use Entware package manager on a Synology storage device.
My dissertation defense on rapid adaptation in snakes has concluded!
Received notification of NSF Postdoctoral Research Fellowship in Biology!
Colored DNA sequence scrolling animation.
Extract CDS and exons sequences from GFF files.
Step-by-step guide to running OrthoMCL ortholog detection software
Understand potential impact of variants based on VEP analysis.
Summarizing various measures about the structure of gene annotations.
A quick-start guide for using gnuplot for in-terminal plotting.
Some notes I made as I began learning forward-time simulation using SLiM
Bash script to download Google Drive file via the command line.
Various Bash one-liners for summarizing variant data
Interactive graphics in Plotly.
Instructions for configuring JBrowse for viewing genome annotations
Thorough guide for performing genome annotation using MAKER.
Instructions for configuring automatic Git pushing when files change. Useful for live coding demos.
Running list of shell one-liners that can be quite useful in genomics.
Automatically detecting and outputing image dimensions from ImageJ.
Useful ImageJ macro that automatically adds scale bars to images
Instructions for modifying RepeatModeler to run more efficiently on sequencing reads
One-liner to calculate proportion missing data per sample in VCF/BCF file.
Some thoughts on best practices for performing reference-guided genome assembly.
Tutorial on batch downloading NCBI SRA files using Bash.
Generating input files for NGSadmix and Entropy.
How-to on doing large downloads of Ensembl data.
How-to on creating BioProjects, BioSamples, and SRA submissions.
Learn bioinformatics in any language using Rosalind.
Announcement of Burmese python genome publication in PNAS!