Comments (1)
Hi, because for this kit the reverse primer is located in FR4
region, the clones are assembled by {FR1Begin:CDR3End}
feature to exclude the primer sequence. If needed you can manually add the following parameter to mixcr analyze
command and then findAlleles
would work:
mixcr analyze invivoscribe-human-dna-ighv-leader-lymphotrack \
--assemble-clonotypes-by VDJRegion \
input_R1.fastq.gz \
input_R2.fastq.gz \
output
from mixcr.
Related Issues (20)
- The majority of results in 'clones_TR[A|B].tsv' are "region_not_covered" HOT 1
- allVHitsWithScore allDHitsWithScore allJHitsWithScore allCHitsWithScore HOT 1
- FASTQ and BAM give discordant results HOT 6
- Help with TCR-seq alignment rate
- findAlleles get empty clone data HOT 11
- Rhapsody BCR+TCR full length data input HOT 2
- Generating all all_contig_annotations.json to run enclone after MiXCR
- Postanalysis output explanation HOT 3
- Runtime error of "Can't apply step BuildingInitialTrees" when running findShmTrees HOT 3
- Question: Does mixcr take sequence stagger into consideration? HOT 1
- ERROR: picocli.CommandLine$ExecutionException: Error while running command align java.lang.IllegalStateException: Check failed. HOT 6
- Importing new whitelist for parsebio protocols
- Long CDR3 sequences HOT 1
- when I used mixcr to analyze RNAseq data, there was an error "unknown options" HOT 1
- Downsampling output missing
- QIAgen Targeted library HOT 1
- overlapScatterPlot output correlation coefficient and p values
- Han el all preset HOT 5
- Pre-Clonotypes HOT 1
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from mixcr.