How to add enzyme details in Tassel pipeline?
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3.3 years ago

Hello All, I working on GBS pipeline, I want to add enzyme details for NlaIII_HaeIII in the source file in tassel pipeline.

For example

 } else if (enzyme.matches("(?i)haeiii-ecor[i1]|(?i)hae3-ecor[i1]")) {
            theEnzyme = "HaeIII-EcoRI"; // GG^CC   G^AATTC
            initialCutSiteRemnant = new String[]{"CC"};
            likelyReadEnd = new String[]{"GGCC", "GAATTC", "GAATTAGATC"}; // look for HaeIII site, EcoRI site, or common adapter for EcoRI
            readEndCutSiteRemnantLength = 5;   

I bit of confusing how to add this kind of chunk for NlaIII_HaeIII

please help

GBS Tassel GBSEnzyme.java • 495 views
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