161210 Struggling with Star - npslindstrom/DE-analysis GitHub Wiki

Today I have been keeping on trying to run STAR to remap the reads of the first sample to the reference genome GRCh38. I am making progress but it is still challenging. I previously tried to extract the new reference genome GRCh38, I tried to do it directly in the terminal using the gunzip command but it only resulted in the entire terminal freezing up, so today I tried to unzip it using sbatch and slurm. At the time of writing this I do not have access to a computer with a unix terminal so I cant see the results but I got a few e-mails from Slurm that suggest something did not work out. I will have to look into it on monday. I will also publish the script I used here for future reference.

While waiting for the reference genome to unzip I wrote a script for using star to generate indices for the mapping step. I basically copied the code given in the manual for STAR. I will publish that here as well as soon as I get access to a computer with a terminal that handles bash.