Preparing, Archiving, and Resurrecting Data To and From Harvard Tape Storage
How to use Harvard’s tape storage with your data.
Performing the Bonferonni and Benjamini–Hochberg Procedures on a Large Dataset
How to control the false discovery rate without relying on R.
Installing RepeatModeler & RepeatMasker
A guide for installing popular repeat annotation software.
Purging Phylogenetic Redundancy
Subsetting a phylogeny non-randomly based on genetic distance.
Genomics Data Management and Compression
Best-practices guide for managing and minimizing the storage footprint of genomics data.
Repeat Annotation using RepeatModeler and RepeatMasker
Thorough guide for annotating and masking repeats using RepeatModeler/RepeatMasker.
Making Axis Text run Downwards in ggplot2
How to run text downward instead of rotating it vertically
Optimizing Augustus
Thorough guide for optimizing Augustus on well-suited BUSCO genes.
Identifying genome-wide RAD-seq loci
A useful script for identifying the footprints of RAD-seq loci from read mappings
A tutorial on whole genome alignment
A thorough tutorial on performing whole genome alignment with the Lastz/MultiZ pipeline
Configuring CPAN on Harvard Odyssey cluster
Notes for how I configured CPAN on Harvard Odyssey cluster
A Brief Introduction to msprime
Notes from a quick introduction session I attended on msprime
Removing Space in Box Sync Folder
How to remove the annoying space in the default Box Sync folder
Relinking ZotFile Attachments
How to re-establish ZotFile links to PDF attachments
Introductory RAD-seq Activity
Experimental design activity to accompany an introductory lesson on RAD-seq
Determining whether RNA-seq data is stranded
How-to guide on quickly determining whether RNA-seq data is stranded
Presented Preliminary Results on Lerista Limb Reduction at Genome10K meeting
Invited to present work as part of comparative genomics session joint meeting of VGP and EBP.
Rattlesnake genome published in Genome Research
Genome provides insight into reptilian microchomosomes, venom gene regulation, and sex chromosome evolution.
Recap of Time in Australia
Accomplished a lot and had some fun in Australia!
Embedding Gist into webpage Markdown
How-to on imbedding Gist content into Minimal Mistakes markdown blog post.
Visualizing Genome Annotations
Creating a UCSC Genome Track for Viewing Genome Annotations
Touchdown in Australia!
I have arrived ‘down under’ to begin postdoc research.
Extracting conserved regions from PhastCons
Extracting conserved regions sequences from PhastCons conservation tracks.
Notes from running Provean
Notes from work installing and running Provean to predict protein impact of variants.
BaseSpace CLI Quickstart
Installing, authenticating, and downloading using BaseSpace CLI.
Invasive Florida Burmese python paper published!
Our paper on rapid adaptation in invasive Burmese pythons published in Molecular Ecology!
Extracting paired FASTQ read data from a BAM mapping file
Details on acquiring reads from BAM file
Setting up and using Entware on Synology device
Use Entware package manager on a Synology storage device.
Dissertation Defended
My dissertation defense on rapid adaptation in snakes has concluded!
Awarded NSF Postdoc Research Fellowship
Received notification of NSF Postdoctoral Research Fellowship in Biology!
Creating a scrolling DNA sequence visualization
Colored DNA sequence scrolling animation.
Extracting spliced sequences from GFF files
Extract CDS and exons sequences from GFF files.
Tutorial for running OrthoMCL
Step-by-step guide to running OrthoMCL ortholog detection software
Variant Effect Analysis using VEP
Understand potential impact of variants based on VEP analysis.
Summarizing the structure of gene annotations
Summarizing various measures about the structure of gene annotations.
gnuplot quickstart guide
A quick-start guide for using gnuplot for in-terminal plotting.
Introductory walkthrough of SLiM
Some notes I made as I began learning forward-time simulation using SLiM
Google Drive download from command line
Bash script to download Google Drive file via the command line.
Useful One-liners for Calculating Population Genetic Statistics from VCF files
Various Bash one-liners for summarizing variant data
A nice introduction to Plotly
Interactive graphics in Plotly.
Configuring JBrowse
Instructions for configuring JBrowse for viewing genome annotations
Genome Annotation using MAKER
Thorough guide for performing genome annotation using MAKER.
Setting-up automatic Git pushing upon file change
Instructions for configuring automatic Git pushing when files change. Useful for live coding demos.
Useful genomics one-liners
Running list of shell one-liners that can be quite useful in genomics.
Image dimensions from ImageJ
Automatically detecting and outputing image dimensions from ImageJ.
ImageJ macro for adding scale bars automatically
Useful ImageJ macro that automatically adds scale bars to images
Running RepeatModeler more efficiently on sequencing reads
Instructions for modifying RepeatModeler to run more efficiently on sequencing reads
Quantify missing data in VCF file
One-liner to calculate proportion missing data per sample in VCF/BCF file.
A (still in progress) best practices workflow for reference-guided genome assembly
Some thoughts on best practices for performing reference-guided genome assembly.
SRA Batch download
Tutorial on batch downloading NCBI SRA files using Bash.
Population structure analysis input file generation
Generating input files for NGSadmix and Entropy.
Batch Ensembl data download
How-to on doing large downloads of Ensembl data.
Submitting data to the NCBI SRA
How-to on creating BioProjects, BioSamples, and SRA submissions.
Plug for Rosalind Bioinformatics learning resource
Learn bioinformatics in any language using Rosalind.
Burmese python genome published
Announcement of Burmese python genome publication in PNAS!