99_NotesForImprovement

Is it better to use SAMtools after mapping to sort BAM file or to have STAR sort the BAMs before writing them? (Probably the latter since less I/O) -> then just merge the sorted files using samtools (merge expects sorted bams anyway)

Streaming FASTQC made Java crash but this didn't halt the job which is problematic (eventually was killed because job time limit was exceeded). Need to increase efficiency. 
-> worked fine when increased memory to 10 Gb and ran on each end of each lane.

Samtools sort on largest BAM took 104 sec and 200MB of memory on the cluster. Need to do some finicky stuff to get it to run as a job array though (or should I just send them as individual jobs? only 192 of them...).