Cuffcompare Class Codes

[jdanderson]

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

[jdanderson]

Here is an example of my modified Ensembl .gtf file:

chr18 protein_coding exon 3507955 3508283 . + . gene_id "ENSMUSG00000024232"; transcript_id "ENSMUST00000025075"; exon_number "1"; gene_name "Bambi"; transcript_name "Bambi-201";
chr18 protein_coding CDS 3508208 3508283 . + 0 gene_id "ENSMUSG00000024232"; transcript_id "ENSMUST00000025075"; exon_number "1"; gene_name "Bambi"; transcript_name "Bambi-201"; protein_id "ENSMUSP00000025075";
chr18 protein_coding start_codon 3508208 3508210 . + 0 gene_id "ENSMUSG00000024232"; transcript_id "ENSMUST00000025075"; exon_number "1"; gene_name "Bambi"; transcript_name "Bambi-201";
chr18 protein_coding exon 3511255 3511542 . + . gene_id "ENSMUSG00000024232"; transcript_id "ENSMUST00000025075"; exon_number "2"; gene_name "Bambi"; transcript_name "Bambi-201";
chr18 protein_coding CDS 3511255 3511542 . + 2 gene_id "ENSMUSG00000024232"; transcript_id "ENSMUST00000025075"; exon_number "2"; gene_name "Bambi"; transcript_name "Bambi-201"; protein_id "ENSMUSP00000025075";
chr18 protein_coding exon 3511980 3516402 . + . gene_id "ENSMUSG00000024232"; transcript_id "ENSMUST00000025075"; exon_number "3"; gene_name "Bambi"; transcript_name "Bambi-201";
chr18 protein_coding CDS 3511980 3512395 . + 2 gene_id "ENSMUSG00000024232"; transcript_id "ENSMUST00000025075"; exon_number "3"; gene_name "Bambi"; transcript_name "Bambi-201"; protein_id "ENSMUSP00000025075";
chr18 protein_coding stop_codon 3512396 3512398 . + 0 gene_id "ENSMUSG00000024232"; transcript_id "ENSMUST00000025075"; exon_number "3"; gene_name "Bambi"; transcript_name "Bambi-201";

Cheers,
Johanthon