Entering edit mode
3.3 years ago
mathavanbioinfo
▴
80
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