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Old 04-12-2013, 01:16 AM   #2
not just another member
Location: Belgium

Join Date: Aug 2010
Posts: 264

I you have a bam file from an aligner (you used bowtie, but you should use a splice-aware aligner like tophat or STAR) and a gtf (or gff) from cufflinks, you can use IGV to visualize the alignment and check the annotation created by cufflinks.
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