RNA-seq- Alternative spliceforms

Question

[pixie@bioinfo]

Hello,

I am interested in identifying alternative splice forms from my RNA-seq data ( mutant and wild type samples with 3 replicates each) . We have generated the gene gtf file from ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG3.2_release/ITAG3.2_gene_models.gff

Unfortunately, I am unable to find the corresponding transcript annotations for the corresponding genes. Is there a way to generate the isoform annotations from the gene .gtf files ?

Thanks

[Eric Lim]

The gff you posted has mRNA entry and that's probably what you're looking for.