De novo genes 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 genes the RPKMs were calculated as sum of RPKMs of all transcripts of a gene. 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