Originally posted by sdriscoll
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You have to provide Subjunc your entire read dataset. Subjunc firstly uses all the junction reads to discover exon-exon junctions and then it uses the discovered junctions to re-align the reads.
Subjunc needs at least 16bp to identify exons. Your read has only 9 bases in the second exon, so providing this read only to Subjunc will not let it find that junction.
Cheers,
Wei
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