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Old 05-26-2016, 06:51 PM   #10
danwiththeplan
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Location: Auckland

Join Date: Sep 2011
Posts: 72
Default Strand specificity

Hi, just to clarify a question about strand specficity.

In Illumina Truseq system, the + strand is digested and the - strand is retained, and that's how strand specificity is maintained, such that only the - strand is sequenced (since the + strand is digested).

So for example, when running htseq-count you would count using the -reverse option (rather than the -no or -yes option) which says that htseq-count expects that the reverse strand is the only one sequenced.

In this system, which strand is retained? or, if this isn't how it works, how do you distinguish the strands ?
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