changes.mady.by.user Micha Sammeth
Saved on Oct 21, 2013
...
http://www.broadinstitute.org/cancer/cga/tools/rnaseqc/examples/gencode.v12.annotation.patched_contigs.gtf.gz
ANNOTATION_FILE gencode.v12.annotation.patched_contigs_sorted.gtf
COUNT_ELEMENTS [SPLICE_JUNCTIONS, INTRONS]
ANNOTATION_MAPPING AUTO
flux-capacitor -p <parameter_file> -i <sample.bam> -o <output.gtf>