QC ALERT

[drosop]

Dear MiXCR team,

I have run the mouse BCR sequencing using Takara SMARTer® Mouse BCR IgG H/K/L Profiling Kit and did analysis using the MiXCR preset mixcr analyze takara-mouse-rna-bcr-smarter using MiXCR v4.5.0. Also, There was very low adaptor content, so I didnt do trimming before.

In the output, I have alerts for :

Successfully aligned reads: 97.67% [OK]
Off target (non TCR/IG) reads: 1.8% [OK]
Reads with no V or J hits: 0.49% [OK]
Overlapped paired-end reads: 32.07% [ALERT]
Reads used in clonotypes: 19.68% [ALERT]
Alignments that do not cover VDJRegion: 68.03% [ALERT]
Alignments dropped due to low sequence quality: 0.0% [OK]
Clones dropped in post-filtering: 0.0% [OK]
Alignments dropped in clones post-filtering: 0.0% [OK]

However, the alignment rate is good. Is this report fine? What can be the reason for low number of reads used in clonotypes or VDJ regions?

Thank you,

[MiLaboratoriesSupport]

​Hi, My guess is that you used a shorter reads' length (150+150?) which was not enough to cover the whole VDJRegion. By default MiXCR tries to assemble the full-length receptor sequence for this protocol. If that is the case, you may add `--assemble-clonotypes-by CDR3` parameter, to assemble clones by CDR3 region only. ​ Sincerely, Mark