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Hi,
I am trying to find splice junctions using PASSion and SOAPsplice. I used wgsim to generate simulated data from chromosome 17. I get output from both of these tools. I can compare their result together, but I don't know how I can validate found junctions with Ensembl dataset. I downloaded gene annotations from ftp://ftp.ensembl.org/pub/release-66.../homo_sapiens/ genbank database. where is exactly the position of junctions for this chromosome placed in the file? how can I match junction position output of these tools with Ensembl dataset?
I am trying to find splice junctions using PASSion and SOAPsplice. I used wgsim to generate simulated data from chromosome 17. I get output from both of these tools. I can compare their result together, but I don't know how I can validate found junctions with Ensembl dataset. I downloaded gene annotations from ftp://ftp.ensembl.org/pub/release-66.../homo_sapiens/ genbank database. where is exactly the position of junctions for this chromosome placed in the file? how can I match junction position output of these tools with Ensembl dataset?