How to understand the 'targetSequences' and 'readCount' in final results with mixcr-4.4.1

[xmy1990]

Thank you very much at first!

I have two issues with my final results of *.tsv with mixcr-4.4.1:

**How to understand the 'targetSequences' and 'readCount' columns in .clones_TRB.tsv or .clones_IGH.tsv ?
I have found them in the doc:
readCount, Number of reads assigned to the clonotype https://mixcr.com/mixcr/reference/mixcr-export/?h=targetsequences#alignment-specific-fields
targetSequences, Export aligned sequences (targets), separated with comma https://mixcr.com/mixcr/reference/mixcr-export/?h=targetsequences#common-fields

If it's convenient, please help me to explan them in common language!

Thank you very much again for your help!

[mizraelson]

Hi,
targetSequences refers to the sequence used to assemble clones. This sequence depends on the preset that you use to analyze data, and it may vary from CDR3 to the full VDJRegion. If you can share the command you used, I can tell you which assembling feature was used.
readCount is the number of sequencing reads with a certain clonal sequence, i.e., "how many times this clone occurred in the sample."

Sincerely,
Mark

[xmy1990]

Thank you very much ！

The command I used:
mixcr analyze exome-seq
--species hsa
--threads 8
$bam
$prefix

As :https://mixcr.com/mixcr/reference/overview-analysis-overview/#cdr3-extension
Can I say: targetSequences is the CDR3 in the left figure and nSeqCDR3 is the CDR3 clustering in the right figure.

Thank you very much again for your help!

[mizraelson]

For exome-seq, the clones are first assembled by CDR3, but later mixcr assembleContigs is used to assemble the longest possible clonal sequence. Because reads in exome-seq randomly cover the clonal sequence, for some clones, it will be possible to assemble only the CDR3 sequence, while for others (more abundant), it may be possible to assemble a longer sequence.
Thus,

• targetSequences in this case refers to the longest sequence that was possible to assemble for a particular clone.
• nSeqCDR3 is the nucleotide sequence of the CDR3 region.

For some clones, targetSequences equals nSeqCDR3.
Let me know if you have any more questions.

Sincerely,
Mark