Hello Everyone,
In my CuffCompare analysis all the class codes in the .tmap file are all "="...."Complete match of intron chain". I used the -r function with a converted Ensembl file. The rest of my expression analysis appears to be valid. Does anyone have any idea what would cause all transcripts to be classified as "Complete match of intron chain"? Is this perhaps a formating issue with the Ensembl .gtf file?
Cheers,
Johnathon
In my CuffCompare analysis all the class codes in the .tmap file are all "="...."Complete match of intron chain". I used the -r function with a converted Ensembl file. The rest of my expression analysis appears to be valid. Does anyone have any idea what would cause all transcripts to be classified as "Complete match of intron chain"? Is this perhaps a formating issue with the Ensembl .gtf file?
Cheers,
Johnathon
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