Hi I am a PhD Student and I am trying to analyze my TRVB data with platforma. The think is that we used our custom library instead of preset kits and to run the clonotype extraction in platforma, the yaml. file with the code seems to be needed.
We usually analyze our data with the following code (in java environment):
java -jar mixcr.jar align --species hsa -p generic-amplicon --floating-left-alignment-boundary --rigid-right-alignment-boundary J --dna -O vParameters.geneFeatureToAlign=“VGeneWithP” -O vParameters.parameters.floatingLeftBound=false -O jParameters.parameters.floatingRightBound=false --report “XXX.report” --json-report “XXX.json” “R1” “R2” “XX.vdjca”
My library amplifies the CDR3 beta
How can I manage it to generate the yaml. file to add to platforma?
Thank you