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ExpressionAnalysis / STAR-SEQR

RNA Fusion Detection and Quantification
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Primer design #4

Closed jasper1918 closed 8 years ago

jasper1918 commented 8 years ago

Currently primer design takes the assembled contig and tries to make primers on each half. Rather, it should ensure that each primer comes from a side of the junction. Either assemble each side separately and join or pull sequence from indexed fasta for the coordinates.

jasper1918 commented 8 years ago

Program now takes an indexed fasta to extract sequences around the breakpoint and passes this to primer design. Leaving this open now, as I may make this optional...

jasper1918 commented 8 years ago

Code only uses the fasta now to design primers and will not use the assembly going forward. Closed