Artificial Diversity Correction

[bshim181]

Hello,

I am running generic-amplicon preset for my TCR data with UMI length of 12. I am getting high percentage of aritifical diversity eliminated and was wondering why this might be.

I am wondering if I specified the parameters wrong. This is what my read architecture resembles.

This is the parameter that I executed.

tag_pattern='^(UMI:N{12})(R1:)^(R2:)'
java -Xmx60g -jar $mixcr analyze generic-amplicon-with-umi
--species hsa
--assemble-clonotypes-by CDR3
--export-productive-clones-only
--rna
-f
--tag-pattern $tag_pattern
-Massemble.cloneAssemblerParameters.addReadsCountOnClustering=true
--rigid-left-alignment-boundary
--floating-right-alignment-boundary C
${R1_file}
${R2_file}
${out_dir}/${filename_woExt}_${run}/${filename_woExt}

[mizraelson]

Hi, the results look fine, the important thing here is that the records weight accepted is 98.68%, meaning most of the reads were ppreserved.