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

<img alt="" src="https://lh5.googleusercontent.com/-nXGQpWfXr0w/U4XSUq5xqDI/AAAAAAAAAHc/0nWXlKgjvNE/s1600/problem3_3UTR.png" style="height:539px; width:808px" />
<p>Hi everyone,</p>

<p>I realized that it is a problem of Cufflinks version (v.2.0.2). Using newer versions, terminal exons are correctly assembled.</p>
