Cufflinks HIDATA

[rhcr56]

Hello all,
I have been using the tophat/cufflinks approach to analyze some fetal and neonate liver mRNA sequence and I have run across the issue of 'HIDATA' in the FPKM status column. The issue I'm having is that most of the genes of interest (albumin, alphafetoprotein, apolipoproteins, etc) all have the HIDATA status in cuffdiff output and thus have FPKM values of zero. My questions are as follows:
1) Why does cufflinks have difficulty testing those genes with a high number aligned fragments?
2) Has anyone encountered this phenomenon, and, if so, how did you address the issue?
Thanks

[jk1124]

I am also wondering this. Did you ever find an answer?

[transcriptome]

Did anybody find a solution for that? I am having the same problem and tried anything possible with the program.

[jk1124]

I think this may be the answer, from the Cufflinks homepage, regarding the 1.1.0 release:

"Some users have reported that Cufflinks or Cuffdiff crashes due to running out of memory when processing highly expressed loci. Both programs now have a maximum number of fragments that can fall within a locus. If a locus has more than this maximum, it is skipped. The threshold is configurable via the --max-bundle-frags option. "

[transcriptome]

Thank you for your reply. I just started the program with that option. Hopefully it will work..

[transcriptome]

That option solved the problem. I got the most highly abundant gene finally in the cufflinks results. Thanks!