techblog2022-05-20
Basics of GO Terms
GO analysis is a widely used analytical method, but to understand it properly you first need to understand GO itself. This post covers the fundamentals of GO Terms.
techblog Articles - Page 7
techblog2022-05-20
Queries on Interval Data
Notes on tools and data structures for performing queries on interval data
techblog2022-05-20
Phylogenetic Analysis Using Maximum Likelihood with MUSCLE + trimAl + RAxML-ng-mpi
Protein-based phylogenetic analysis is a well-known and important method for studying gene function and evolution. In this post, we create a multiple alignment using MUSCLE, remove non-conserved regions with trimAl, and then perform phylogenetic analysis using the maximum likelihood method with RAxML.
techblog2022-05-20
Submit Commands Directly as Jobs via qsub
When using a supercomputer, you often need to submit jobs via qsub. Sometimes you just want to run a one-liner, and having to create a script file first is tedious. Here, I use Python's argparse and subprocess to pseudo-submit commands as jobs directly from the command line.
techblog2022-05-20
Reading and Writing fastq/fastq.gz in Rust
Reading and writing fastq/fastq.gz files using rust-bio.
techblog2022-05-20
Processing Salmon Output Files with tximport
Salmon's output file is quant.sf, and processing it can be quite complex with many possible approaches. This article summarizes the various output formats and use cases available through tximport.
techblog2022-05-20
Tips for Downloading FASTQ Files from SRA
Tips and related knowledge for downloading FASTQ files from SRA
techblog2022-05-20
Uploading Data to SRA Using Aspera
Uploading data to SRA via HTTP or FTP is far too slow, so let's use IBM's Aspera Connect for faster uploads.
techblog2022-05-20
The Story of How I Lost Money by Not Releasing an Elastic IP Address on AWS
A cautionary tale about getting billed by AWS after leaving resources running when you're done playing around
techblog2022-05-20
Deploying to Heroku with FastAPI + SQLAlchemy (Postgres)
I wrote this because I couldn't find many articles focused solely on deploying with FastAPI and Postgres to Heroku.