Recent Posts
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. To check whether the desired volume has a noexec flag:
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 NovaSeq systems require user-developed or third-party data analysis tools, such as bcl2fastq, to be converted into FASTQ. Aside from enabling the conversion of BCL files into FASTQ, bcl2fastq can also assign sequencing data to specific samples based on their barcode (demultiplexing), trim adapters and Unique Molecular Identifiers (UMIs), and include the UMIs in the read names within the FASTQ files.
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 about the code underlying the colored maps. Given the biological nature of the data that I regularly work with, I already abandoned all hope of making such fancy maps out of genuine necessity—not until the unveiling of the dataviz challenge of David McCandless of Information is Beautiful and the World Government Summit. I have no intention of participating, but I love me some tidy data that I can cop without scraping. Now on to the code:
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 financial aid to take Andrew Ng’s Machine Learning course in Coursera. Having been a victim of the all too common case of very smart people being unable to explain themselves well and given Ng’s caliber, I didn’t think I would be able to wrap my head around the lectures. I’m on my 8th week now, and it’s honestly one of the things I look forward to when weekends roll around. However, my brain’s wiring dictates that my understanding of any concept only becomes granular when I force myself to write about it. Here is an attempt at linear regression and gradient descent.
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 similar to the regular MiSeq except it has a forensic genomics mode. Together with our friends from the UP Natural Sciences Research Institute (NSRI), we performed an in-house bench test of our new toy. The absence of the need to spend additional money and the demand to perform machine validation made up the perfect excuse to get ourselves genotyped. Come to think of it, there is no way I am ending my stint in the Philippine Genome Center (PGC) without having my genomic DNA sequenced one way or another.