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GTEx runs

Flux Version

Flux-Capacitor v1.2.3 (Flux Library: 1.20)

Annotation File

The quantifications are based on a modified Gencode (v12) version created at the Broad Institute:

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

 

Parameter File

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

Command Line

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