• Functions on a Google Documents Table

    Today I had to make an expense report and decided to use a Google document instead of a spreadsheet so I could embed images of all receipts as I went. I knew Google documents had tables and figured that they had simple functions like SUM. They did not. What they did have was Google Apps Script found under Tools -> Script Editor. I had a hard time with the tutorials, but I’m sure this project is still maturing and might be dropped from Google’s offerings any day. However, I did manage to make a script (with a button!) that sums dollar values in a table and prints the total in the last row.

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    09 Jun 2014

  • FASTQA-JS

    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.

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    29 May 2014

  • Exponential Growth of NCBI Genomes

    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.

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    31 Mar 2014

  • Recomb 2014

    I will be presenting a poster at http://www.compbio.cmu.edu/recomb/ this year.

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    20 Feb 2014

  • Genome Browsers

    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.

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    23 Jan 2014