with cufflinks, can there be "0" fpkm value and yet full read support?

[velu]

Hi,
I used hisat2 (2.0.5) to map 150b Paired-end reads on to the draft genome of castorbean and used cufflinks (version 2.2.1) to perform reference annotation based transcript assembly (RABT). This data is NOT for differential expression analysis. The assembler reported novel isoforms and some novel genes. From the results, of the transcripts that were as present in the gtf file used for RABT, some had an FPKM value of "0.0000000000" but were "yes" for "full_read_support" whereas the rest that were "yes" for "full_read_support" carried an FPKM value at 1 or above.
Could anyone please explain why would a transcript be described as present with "full_read_support," yet with an FPKM value of "0.0000000000?"

Thanks.

[Dario1984]

I have noticed similar problems with Cufflinks in the past. Our research group no longer uses it because it hasn't been updated in 3 years and some of the FPKM values look suspicious, which you have noticed.

[velu]

Thank you, Dario1984.
Then, what method do you follow for the assembly of reads that do not have such limitations?

[Dario1984]

We use Trinity because we found its results can be experimentally validated by biologists. There's also a genome guided assembly mode. It was developed a few years ago, but it still maintained by the developer. You might also be interested in categorising your assembled transcripts with TransDecoder.

[velu]

Thank you.
I will go through the possibilities you have suggested.