Closed Dharmendra-G-1 closed 4 years ago
Hi Dharm,
First of all, I recommend using official MiXCR docker image milaboratory/mixcr
(link).
I also recommend using analyze
command to process the data (link).
All the CDR3's are in the file, in nSeqCDR3
and aaSeqCDR3
columns.
Regarding C-genes: our IMGT converted library does not include their sequences, so they will not be mapped for pig data.
I am working on the non-human sample, i.e. pig RNASeq data to get its TCR repertoire characterized. For this, I am using a docker version of mixcr.
docker run -it --rm -v $PWD:/output -w /output mgibio/mixcr /bin/bash
I downloaded the imgt.201918-4.sv5.json.gz from https://github.com/repseqio/library-imgt/releases
unzip imgt.201918-4.sv5.json.gz
Once inside the mixcr docker image , I placed this imgt.201918-4.sv5.json in libraries folder of the mixcr docker image then run the following command to process the sample whose pair fastq files are stored in seqs/ directories.
Then inside
I was expecting to have a T cell Receptor Beta receptors seq (TRBV, TRBD and TRBJ genes) mapped but that result file missing all "allCHitsWithScore" column in the clones.txt
excerpt of clones.txt
head clones.txt
The Report file is as follow for reference:
Can you please help to find why I am missing alignments and column with the value for CDR3 (T cell Receptor Beta; TRBV, TRBD and TRBJ genes), is there a parameter I need to change?, any parameter in the command so that RNASeq reads aligned to pig T cell Receptor Beta and other missing TR:
More information: http://www.imgt.org/IMGTrepertoire/LocusGenes/repertoires/pig/TRB/Susscro_TRBrep.html
Gene table: Pig (Sus scrofa) TRBV Gene table: Pig (Sus scrofa) TRBD Gene table: Pig (Sus scrofa) TRBJ Gene table: Pig (Sus scrofa) TRBC Locus description: Pig (Sus scrofa) TRB
Thanks,
Dharm