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http://www.broadinstitute.org/cancer/cga/tools/rnaseqc/examples/gencode.v12.annotation.patched_contigs.gtf.gz

Parameter File

 

ANNOTATION_FILE gencode.v12.annotation.patched_contigs_sorted.gtf
COUNT_ELEMENTS [SPLICE_JUNCTIONS, INTRONS]
ANNOTATION_MAPPING AUTO
 

Command Line

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flux-capacitor -p <parameter_file> -i <sample.bam> -o <output.gtf>

 

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