Contig Calling (Annotation Agnostic):  Contigs represent the union of the qualified/post-filtered mapped reads from each biological replicate.  Each contig gets a score representing the sum of the reads from both bioreps.  Contigs with only a single read (0,1; 1,0) are discarded.  The surviving contigs are then independently scored for each replicate according to their mapped read count.  These values are used to compute Non-parametric-IDR (A Dobin, CSHL) values for each contig.  These results are reported in .BED format.

.BED Format:
Column 1: Chromosome ID
Column 2: Contig Start
Column 3: Contig Stop
Column 4: Contig Name (named by co-ordinates)
Column 5: Contig Expression Score (RPKM computed using the summed reads from both bioreplicate. Value capped at 1,000). 
Column 6: Strand
Column 7:  Real RPKM (non-capped)
Column 8: IDR score (.dot if there is only 1 replicate)
Column 9: Sum of the read counts for both biological replicates. 

Generated by: Wei Lin, CSHL

Contact: Carrie Davis (davisc@cshl.edu) and Wei Lin (wlin@cshl.edu)