Unfiltered GEM read mappings were employed, after converting them to BED format.
The quantifications are based on the Gencode (v12) reference annotation:
ANNOTATION_FILE gencode.v12.annotation.gtfREAD_DESCRIPTOR {ID}/{MATE}[1,2]ANNOTATION_MAPPING PAIRED |
flux-capacitor -p <parameter_file> -i <sample.bam> -o <output.gtf> |
To speed up computation of the big dataset, the JIP pipeline system has been employed. All datasets were quantified in parallel, splitting each dataset on a per-chromosome base.