Hey all,
I'll try to quickly explain my problem.
I am working on rice, which is poorly annotated, and following the Tuxedo Nat Meth paper form Cole.
I have 120 RNAseq samples (which have been ribotreated), and use cuffmerge, to produce a unique GTF file.
The problem is that cuffmerge produces too many of isoforms, which results in very low number of differentially expressed genes after cuffdiff
(quote form Cole: In general, the more isoforms a gene has, the more uncertainty there will be in assigning reads to each isoform, and the more uncertainty there will be in the overall gene expression level. That means more variance, so if you have a ton of isoforms (possibly because of a bad assembly), you'll see very few differentially expressed genes.)
Do you have any solutions for that, apart from using the poorly annotated original gtf file ?
Thanks a lot.
David
I'll try to quickly explain my problem.
I am working on rice, which is poorly annotated, and following the Tuxedo Nat Meth paper form Cole.
I have 120 RNAseq samples (which have been ribotreated), and use cuffmerge, to produce a unique GTF file.
The problem is that cuffmerge produces too many of isoforms, which results in very low number of differentially expressed genes after cuffdiff
(quote form Cole: In general, the more isoforms a gene has, the more uncertainty there will be in assigning reads to each isoform, and the more uncertainty there will be in the overall gene expression level. That means more variance, so if you have a ton of isoforms (possibly because of a bad assembly), you'll see very few differentially expressed genes.)
Do you have any solutions for that, apart from using the poorly annotated original gtf file ?
Thanks a lot.
David
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