Hello,

I used Cufflinks (v.2.0.2) to assemble a complete transcriptome without providing any GTF references just to check the quality of assembly and it seemed to work so well, but I am worried several terminal exons were not entirely reconstructed (see attached figures in which I compared my cufflinks results with RefSeq annotations using IGV browser) although read coverage was quite good. I tried to change several parameters (disabling low-coverage 3' trimming; decreasing minimum reads per transfrags, min-isoform-fraction, or small-anchor-fraction) but the problem persisted.

Did somebody have the same problem or know how to fix it?

Thanks, Jorge