Calculating Mapping Statistics from a SAM/BAM file using SAMtools and awk
A BAM file is the binary version of a SAM file, a tab-delimited text file that contains sequence alignment data. Mapping tools, such as Bowtie 2 and BWA, gen...
Posts by Category
AWK
Bioinformatics
Calculating Mapping Statistics from a SAM/BAM file using SAMtools and awk
A BAM file is the binary version of a SAM file, a tab-delimited text file that contains sequence alignment data. Mapping tools, such as Bowtie 2 and BWA, gen...
Simulating Sequence Reads from a Reference Genome with wgsim
wgsim is a tool within the SAMtools software package that allows the simulation of FASTQ reads from a FASTA reference. It can simulate diploid genomes with s...
Linux
Solution: Unable to execute a script on a mounted external drive on Linux
If you’re unable to execute a script on a mounted external drive on Linux, it’s likely that a noexec flag has been invoked during the mounting of the disk. T...
Compiling bcl2fastq v2.20 on Ubuntu 18.04
Unlike the MiSeq which automatically converts binary base call (BCL) files into FASTQ format using the MiSeq Reporter, output from the NextSeq, HiSeq, and No...
Ubuntu 14.04 Login Loop and Missing Desktop Icons
After restarting my desktop the other day, I found Ubuntu 14.04 stuck in a login loop. It was not the first time this problem had reared its ugly head, and l...
How to Run a Process as a Background Task
To my disappointment, much of my experience in wrangling DNA sequences involves short bacterial genomes. My workstation, which features a 4.0-GHz 8-core proc...
Machine Learning
Linear Regression and Gradient Descent
Some time ago, when I thought I didn’t have any on my plate (a gross miscalculation as it turns out) during my post-MSc graduation lull, I applied for a fina...
NGS
Getting Genotyped with the Illumina ForenSeq Kit and MiSeq FGx
A month ago, our facility had the opportunity to try our hand at the Illumina ForenSeq DNA Signature Prep Kit which came with our MiSeq FGx. The MiSeq FGx is...
Phasing Technologies (10x Genomics Chromium and Dovetail Genomics Hi-C)
Last January, I had the privilege of attending the Plant and Animal Genome Conference XXVI in San Diego, California. My boss calls it the only essential agri...
R
Making Maps with ggplot2
I remember looking at Freedom House’s beautiful (but alarming) set of visualizations on the status of global democracy in 2018 with a burning curiosity abou...
Linear Regression and Gradient Descent
Some time ago, when I thought I didn’t have any on my plate (a gross miscalculation as it turns out) during my post-MSc graduation lull, I applied for a fina...
Replicating WEGO Plots using ggplot2
WEGO (Web Gene Ontology Annotation Plot) is a tool for visualizing, comparing, and plotting gene ontology (GO) annotation results. WEGO accepts various file ...
R: Some Table Munging Tricks
I’ve been working with huge tables lately (at least 50,000 rows or columns). Sometimes you think you know all the basic commands you need to string together ...
On Hadley Wickham, the Prolific R Developer
I spent the entire November writing scripts to generate the figures for my thesis and finding ways to make my data appear lovely. While it sounds leisurely w...
Warning and Error Handling with tryCatch()
A few weeks ago, I worked on an implementation of Fisher’s exact test in R. The script expects a data frame with rows representing the various cases/phenotyp...
Statistics
Linear Regression and Gradient Descent
Some time ago, when I thought I didn’t have any on my plate (a gross miscalculation as it turns out) during my post-MSc graduation lull, I applied for a fina...
Standard Deviation and Variance
One of the tools that we discussed in our Data Analytics class last week was canonical correlation analysis (CCA). I won’t delve into CCA as I haven’t fully ...