Differential Isoform Expression In Cuffdiff: How Does It Work?
I am running an analysis in CuffDiff using a GFF file of annotations from FlyBase www.flybase.org). The GFF file contains annotation data for genes, mRNA, CDS and 5'- and 3'-UTR's.
Differential expression of isoforms is reported in some 1266 pairwise comparisons. However, most of the genes in the analysis contain only 1 transcript; and there is very little overlap between the genes showing differential expression (file gene_exp.diff) and the isoforms showing differential expression (file isoform_exp.diff). Can any one explain to me how this is possible?
• 3,865 views
•
link
written
by
gwilymh1000 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Question: Cuffdiff output file gene_exp.diff has only one gene but isoforms_exp.diff has thousands …
written by SamuelWarner •
-
IsoformSwitchAnalyzeR and cuffdiff data error
written by dina.hesham139
-
Cuffcompare on the merged GTF file produced by Stringtie
written by seta
-
Why does cuffdiff test differential isoform expression for genes with only one annotated transcript?
written by unsupervised_learner •
-
Cuffmerge:Which samples to use for creating a merged gtf file?
written by EpiExplorer
-
Isoform switch, definition and selection of candidates
written by Lalla •
-
Is it necessery to use GTF annotation exlusively for mRNA if sequencing library is mRNA enriched?
written by AlexAbdulkaderKheirallah
-
Rna Seq Data Analysis
written by sara •
-
Cuffdiff Gene Miss?
written by luwening •
-
Cufflinks / Cuffdiff Output - How Are Tests Different?
written by Stephen
Do you mean to say that there are 1266 transcripts that are significant? How many genes are significant in the same comparison? It will be good if you can provide some sample data (the isoforms/genes)