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Old 12-20-2015, 10:19 PM   #4
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Location: Beijing

Join Date: Nov 2011
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4.2.3 Compatibility with Cufflinks
For unstranded RNA-seq data, Cuinks/Cu di require spliced alignments with XS strand attribute,which STAR will generate with --outSAMstrandField intronMotif option. As required, the XS strand attribute will be generated for all alignments that contain splice junctions. The spliced alignments that have unde ned strand (i.e. containing only non-canonical unannotated junctions)
will be suppressed.
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