mizraelson
commented
5 months ago 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.
Closed bshim181 closed 5 months ago
mizraelson
commented
5 months ago 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.
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} \ ${out_dir}/${filenamewoExt}${run}/${filename_woExt}