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  • tophat junctions strands

    Hello, I did some tophat mapping and looking at the results, it seems that the strand of the junctions that tophat predicts are very much consistent (I would say 90-95% of the time I see it, the junction strand matches the gene strand) with the actual strands that the gene belongs to. I know that the rna-seq data I have is not stranded. Is there an expectation that the junction strands will match the gene's actual strand? Thanks.

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