Flux Version
Flux Capacitor 1.2.3 (Flux Library: 1.20)
Read Mappings
Tophat mappings were employed, filtered for primary alignments (mapper comparison) by samtools
samtools view -bF 256 file.bam > filtered_file.bamAnnotation File
The quantifications are based on a modified Gencode (v12) annotation created at the Broad Institute:
Parameter File
ANNOTATION_FILE gencode.v12.annotation.patched_contigs_sorted.gtf COUNT_ELEMENTS [SPLICE_JUNCTIONS, INTRONS]ANNOTATION_MAPPING AUTO |
Command Line
flux-capacitor -p <parameter_file> -i <sample.bam> -o <output.gtf> |
Overview
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