Right now it’s mostly a waiting game. I’m running tophat2 on my samples to map the reads to the human genome. I have two samples I’m working with: A control group and a Crohn’s Disease (test) group. Each run takes a minimum of around six to seven hours, and some have taken more than a day to complete! After, I run featureCounts on the results to see how many repeats are expressed in each group. This step usually takes less than a minute, so it’s the tophat2 that I’m waiting on. Everything is running smoothly (so far), so that’s great!
See you in my next post!