From Tophat output "junctions.bed", we could know the position of junctions. I think this junction should be intron. But after I assembled tophat output by Cufflinks, I found that the position of intron is different from that of intron.
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Originally posted by scottyler89 View PostA couple of possibilities:
Have you done QC filtering using something like FASTX toolkit? Or maybe, it's just optional exons, or an alternative splice site. Have you looked at the DNA sequence to see if it has possible splice acceptor/donor sites?
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