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Update library parameter assignment in parameters.csv #215

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mmterpstra opened this issue Jun 8, 2015 · 0 comments
Open

Update library parameter assignment in parameters.csv #215

mmterpstra opened this issue Jun 8, 2015 · 0 comments

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@mmterpstra
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The parameter list assumes that every new run is a new library preparation. This might cause artifacts not to be removed by MarkDuplicates. My suggestion is to make this parameter less greedy or track library preparations.

old:

runPrefix   ${sequencingStartDate}_${sequencer}_${run}_${flowcell}
filePrefix  ${runPrefix}_L${lane}
library     ${filePrefix}
#parametric expansion results in:
library     ${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}

new:

#better
library     ${externalSampleID}_${barcode}
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