The 4DN RNA-seq data processing pipeline uses the ENCODE RNA-seq pipeline v1.1. We have modified the logistics of the pipeline execution without changing the content of the pipeline, except we have excluded the Kallisto run which is a dispensible addition to the full pipeline based on STAR/RSEM. In addition, we modified MAD QC to handle more than two biological/technical replicates.
We have run the pipeline individually for each biological/technical replicate, merging only sequencing replicates at the fastq level. The output bam, bw and expression tsv files are generated for each biological/technical replicate. The entire pipeline was run as a single execution unit.
A more detailed description of the 4DN RNA-seq pipeline can be found at :
For more detail, see description/documentation from ENCODE.