Comments (4)
The determination process is somewhat more complex than simply examining the number of reads. Initially, the sequencing quality of the nucleotide is considered. Subsequently, a negative binomial distribution is applied to ascertain if this nucleotide might be the result of an error, accounting for both the read proportion of the clones and the quality of the sequencing.
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Hi,
Could you please provide the exact command you used?
To address your question, we should initially examine the alignments that support each clone. This can be done using the mixcr exportAlignments input.vdjca output.tsv
command. It's likely that there was a comparable number of reads supporting each variant, cause clustering only happens if one clone has a significantly lower count.
Sincerely,
Mark
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I basically used generic-amplicon preset set-ups and made only changes during exportClone parameters (I believe generic-amplicon by default clusters by CDR3 sequences with max mutations allowed being 2 nt mismatches or 1 indels but not both).
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I was wondering since these clonotypes have identical CDR3 seq (with 1 difference in nt) and also identical V and J segments, does it make sense to combine or cluster these clonotypes together?
![Screenshot 2023-07-27 at 10 07 03 AM](https://private-user-images.githubusercontent.com/53489568/256562537-7653728d-fe11-44d1-adbc-323a213808dc.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjM4NTk4ODEsIm5iZiI6MTcyMzg1OTU4MSwicGF0aCI6Ii81MzQ4OTU2OC8yNTY1NjI1MzctNzY1MzcyOGQtZmUxMS00NGQxLWFkYmMtMzIzYTIxMzgwOGRjLnBuZz9YLUFtei1BbGdvcml0aG09QVdTNC1ITUFDLVNIQTI1NiZYLUFtei1DcmVkZW50aWFsPUFLSUFWQ09EWUxTQTUzUFFLNFpBJTJGMjAyNDA4MTclMkZ1cy1lYXN0LTElMkZzMyUyRmF3czRfcmVxdWVzdCZYLUFtei1EYXRlPTIwMjQwODE3VDAxNTMwMVomWC1BbXotRXhwaXJlcz0zMDAmWC1BbXotU2lnbmF0dXJlPTI5YzYyYWZkNzY4MGQ1ZjQzNzljMzc0YTRiNzZlZWQyNTgzNmFlMjgyMzA5ODRlNjU5NDdmY2EyYjcxNzJmY2EmWC1BbXotU2lnbmVkSGVhZGVycz1ob3N0JmFjdG9yX2lkPTAma2V5X2lkPTAmcmVwb19pZD0wIn0.7WXBJcilND2eMChnvh619yhFWmJQVZpGj7PEGTVCq1E)
![Screenshot 2023-07-27 at 10 07 24 AM](https://private-user-images.githubusercontent.com/53489568/256562617-5d1c9473-0032-4d60-a34b-34af80ed182f.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.7yLDbxHpKNFgWr1x9_VyNwCQUNM1kSIhopQzOU6AnxI)
The read count comparison is 284 vs 5. What is the threshold for valid number of reads that support each variant?
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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
- `Feature for allele search doesn't intersect JGene` error when running `findAlleles` HOT 1
- 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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