Problems in the automated transcriptome reconstruction. (A) Transcripts missed, even with full coverage. The red line (pointed out by black arrow) gives an example of a gene with a large amount of reads that was not defined by Cufflinks. Upper part of the plot shows the read coverage, middle part the reads and lower part the transcripts defined by Cufflinks as blue bars. (B) Overlapping transcripts. An example is given of two transcripts overlapping in their 3’ UTRs (one manually and the other Cufflinks defined). The transcripts are represented by red and blue lines and their overlap by a black arrow. Visualization of reads on genome in both panels performed using IGV browser  (http://www.broadinstitute.org/igv/).