Hi. I got the laptop!
I spent the week installing some software onto it. I needed TopHat and BowTie (of course), which seemed pretty straightforward at first. Downloading them was easy but actually installing them was a bit more of a headache. With the help of a nice person and some nice websites, I figured out that to install TopHat, I first needed to install BowTie. To install BowTie, I needed to install Bioconda. Bioconda’s website suggested that I install Miniconda instead, so I did that. It took a while, but in the end, TopHat and BowTie were up and running! Now I just need to figure out how to fix a small error that shows up when I run tophat2.
This week’s main paper was: “Differential genes and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks” by Trapnell et al. You can read it here with me! It’s a protocol paper to give some background on how TopHat and Cufflinks work, as well as commands to use them. One common one that the paper includes is:
$ tophat2 -p 8 -G genes.gtf -o C1_R1_thout –library-type=fr-firststrand \ genome C1_R1_1.fq C1_R2_2.fq
The commands are run in the command line.
See you later!