161208 STAR and Reference Genome - npslindstrom/DE-analysis GitHub Wiki

I have been reading the manual for STAR to see if I can manage to run it on the raw data.

Manual to STAR: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf

I managed to find STAR in the list of available modules on Milou so I will try to run it on UPPMAX. My first thought was to try and run STAR on my home computer but I can't figure out how to install and use it that way. It seems easier to use UPPMAX. However I am not sure as to what project I will submit any sbatch jobs. I will have to ask someone.

I am also think about what reference genome build to use. The standard RNA-seq pipeline that was applied to our data used Tophat and the reference genome GRCh37. This is the old assembly however so I am considering running it against GRCh38 instead. I downloaded the reference genome and tried to unzip it but the terminal froze so I am giving up for today. Will continue the struggle tomorrow.