Clone table fields missing

[Januaryyiyue]

Checklist before submitting the issue:

• The issue is strongly related to the MiXCR software
• The issue can be reproduced with the most recent version of MiXCR
• There is no answer to the question in the official documentation and there is no duplicate issue in the bug tracker
• Inspection of raw alignments with exportAlignmentsPretty shows that data has the expected architecture, and sample preparation artefacts are not the reason of the problem (if this is the matter of the issue)

Expected Result

A clone table with the following fields: cloneId cloneCount cloneFraction targetSequences targetQualities allVHitsWithScore allDHitsWithScore allJHitsWithScore allCHitsWithScore allVAlignments allDAlignments allJAlignments allCAlignments nSeqFR1 minQualFR1 nSeqCDR1 minQualCDR1 nSeqFR2 minQualFR2 nSeqCDR2 minQualCDR2 nSeqFR3 minQualFR3 nSeqCDR3 minQualCDR3 nSeqFR4 minQualFR4 aaSeqFR1 aaSeqCDR1 aaSeqFR2 aaSeqCDR2 aaSeqFR3 aaSeqCDR3 aaSeqFR4 refPoints

Actual Result

Fewer fields than expected" cloneId readCount readFraction targetSequences targetQualities allVHitsWithScore allDHitsWithScore allJHitsWithScore allCHitsWithScore allVAlignments allDAlignments allJAlignments allCAlignments nSeqCDR3 minQualCDR3 aaSeqCDR3 refPoints

Exact MiXCR commands

java -jar /path/to/mixcr.jar align -p rnaseq-cdr3 --verbose -s hsa -OallowPartialAlignments=true -OvParameters.geneFeatureToAlign=VGeneWithP -r /path/to/LOG_ALIGN.txt /path/to/file_R1.fastq /path/to/gile_R2.fastq /path/to/alignments_file.vdjca java -jar /path/to/mixcr.jar assemblePartial /path/to/alignments_file.vdjca /path/to/rescue1_file.vdjca java -jar /path/to/mixcr.jar assemblePartial /path/to/rescue1_file.vdjca /path/to/rescue2_file.vdjca java -jar /path/to/mixcr.jar extend /path/to/rescue2_file.vdjca /path/to/extended_file.vdjca java -jar /path/to/mixcr.jar assemble -r /path/to/LOG_ASSEMBLE_file.txt /path/to/extended_file.vdjca /path/to/file.clns java -jar /path/to/mixcr.jar exportClones --chains TRB /path/to/file.clns /path/to/CLONES_TRB_file.tsv java -jar /path/to/mixcr.jar exportClones -o -t --chains TRB /path/to/file.clns /path/to/PROD_CLONES_TRB_file.tsv

[mizraelson]

Hi, I recommend running the latest version of MiXCR and the following command:

java -jar /path/to/mixcr.jar analyze rna-seq \
-s hsa \
/path/to/file_R1.fastq \
/path/to/gile_R2.fastq \
/path/to/output

It will run all the commands you have, and also assembleContigs that seems to be missing from your pipeline. The output should be as you expected with all regions if covered.

[mizraelson]

Do you have a bulk RNA-seq data?

[Januaryyiyue]

We have hybrid capture DNA-sequencing data of the CDR3 region.

Should I try adding - assembleContigs in the yaml file?

[mizraelson]

Are you talking about CapIG-seq? The library prepared by this protocol does not cover other regions as I understand and primarily is focused on CDR3.

[Januaryyiyue]

I am using capTCR-seq, which only sequences the CDR3 region.

[mizraelson]

Then you can't export columns with sequences of the regions that are not covered.