I ran cufflinks to get the gtf file. How should I get the exon and intron structure of a gene based on the gtf file? I am wanting to map the exon and intron structure identified by cufflinks onto my gff annotation file of the genome.
The GTF file is the (predicted) exon/intron structure. Or do you have some only CUFF* ids and want instead more useful things like gene names and ids?
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