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Old 07-20-2011, 01:20 AM   #4
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Location: Cambridge, UK

Join Date: May 2010
Posts: 311

This might be a trivial advice but worth checking... Are the reference sequence file and GTF file using the same chromosome names? (E.g. ENSEMBL calls chromosomes as 1, 2, 3 etc while UCSC calls them chr1, chr2 ...)

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