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Hello all,
I've been using the tuxedo suite for a while but I recently ran into a weird problem when using cuffdiff to look at splicing. Cuffdiff generated a few thousand significant genes with AS between four of my samples.
The problem is that most of the genes with "significant alternative splicing" only have one isoform and therefore could not even be alternatively spliced!
The genes appear differentially expressed, but how could cufflinks think they have AS when they only have one isoform? These genes are showing up as significant in splicing.diff but when I examine them in isoforms.fpkm_tracking each only has one line.
I've been using the tuxedo suite for a while but I recently ran into a weird problem when using cuffdiff to look at splicing. Cuffdiff generated a few thousand significant genes with AS between four of my samples.
The problem is that most of the genes with "significant alternative splicing" only have one isoform and therefore could not even be alternatively spliced!
The genes appear differentially expressed, but how could cufflinks think they have AS when they only have one isoform? These genes are showing up as significant in splicing.diff but when I examine them in isoforms.fpkm_tracking each only has one line.
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