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 an different versions of Cufflinks were used to assemble and quantify transcritps. The transcripts were assembled using Cufflinks 0.9.0 with the the bio-replicas pooled. To increase the throughput the assembly was done separately for each chromosome. The assembled transcripts (with all chromosomes combined) were then quantified using Cufflinks 0.9.3 separately for each replicate. Bias correction was not used in quantifications. For genes the FPKMs were calculated as sum of FPKMs of all transcripts of a gene. The resulting FPKM1 and FPKM2 values are included as attributes in the GFF file. The IDR was calculated using the signal equal to the product of Cufflinks coverage and length summed for all transcripts of a gene, divided by 152, which aproximately corresponds to the number of read pairs per gene. Contact: dobin@cshl.edu