Week 3: Finding a rhythm
This week was the first week I had actually started to settle into a rhythm, get to the lab at 8:00 work for a few hours then get coffee and go back to working. This week the main goals were to run longranger wgs on sample data and to become familiar with the program gordian, it is the software used to make the bins that I classified earlier.
This however without sudo permissions on the server I was running it on was much easier said than done. I ran into so many roadblocks when trying to install the packages and the subpackages automatically I simply decided it would be faster just to download them by hand, and it was. So I got long ranger and gordian properly installed.
The next few days I spent about half of my time in the wet lab, I got to learn how to analyze the number of living cells in a solution and then I learned how to use the sage. After that we left the sage running and colleen gave me another task. This time instead of using bins to classify what NOTCH region the reads came from she wanted me to be able to make a script that could use VCF files of the samples in order to calculate that information. This took pretty much the rest of the week, and I ended up having to use Varscan and awk to convert some files into VCFs.