To better enable researchers to analyze their own fastq files without downloading additional software, I created FASTQA-JS. Base quality scores often drop off towards the end of a read when errors accumulate in the spots of DNA on a flowcell. It is common practice to analyze these quality scores and truncate the reads when quality scores are below a specified threshold. Below is an example of the output from FASTQA-JS.
Read more...29 May 2014
I have been studying bioinformatics for 4 years and had the privilege to work in a sequencing lab and personally see the technology change and accelerate. When I started work at the CGB in 2010, a whole genome cost around $10,000 to sequence on an Illumina GA II machine. In 2013, the IU Bioinformatics Club resequenced a human genome for $4,000. Now Google’s Calico is pushing for the $1,000 human genome. This price point make whole genome resequencing more affordable than the average trip to the hospital, making personalized medicine very attractive.
Read more...31 Mar 2014
I will be presenting a poster at http://www.compbio.cmu.edu/recomb/ this year.
Read more...20 Feb 2014
For the past few years, I’ve used IGB as my preferred coverage viewer. I appreciated that it was an open-source project, and I could recommend colleagues to use it since it was an open-source project and it was easy enough to launch a java program on any system. Recently, I switched to IGV since the auto-scaling and data transformation features in IGB were not functioning on bedgraph data. As highlighted by the red circles in the figure, low values are hidden in IGB since the y-axis of the data track does not rescale based upon the viewing window.
Read more...23 Jan 2014
I originally wanted to host this site completely on Google Drive using the method laid out at: GoogleDriveHosting. This method was appealing because I could depend on Google’s infrastructure for reliability even though I would be restricting myself to client-side scripting (HTML, CSS, and JavaScript). After some experimentation with public Drive folders, I found out that all communication was loaded over https, so I would not be able to link my domain name for security reasons.
Read more...01 Dec 2013