De novo exons were generated by Cufflinks using STAR alignments.

The BAM alignments files were filtered using 'samtools rmdup -S' command to remove (PCR?) duplicates.

Because of the bugs in 0.9.0-0.9.3 releases different versions of Cufflinks were used to assemble and quantify transcritps.

The transcripts were assembled using Cufflinks 0.9.0 with the bio-replicates pooled.
To increase the throughput the assembly was done separately for each chromosome.
The assembled transcripts (with all chromosomes combined) were then quantified using the flux capacitor (http://flux.sammeth.net/)  
separately for each bio-replicate.

For exons the RPKMs were calculated as sum of RPKMs of all transcripts sharing this exon. 
The resulting RPKM1 and RPKM2 values are included as attributes in the GFF file.
The iIDR (intuitive IDR) was calculated using the RPKM values of each bio-replicate.

Contact: dobin@cshl.edu or sarah.djebali@crg.eu