Discrepancy Between MiXCR CDR3 Sequences and scRNA-seq Data #1485
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I'm encountering an issue while correlating MiXCR and 10x Genomics scRNA-seq data. After running Could MiXCR's processing lead to CDR3 sequences that don't match raw RNA-seq reads? Appreciate any insights or suggestions! |
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Hi, MiXCR processing can't create a CDR3 sequence that was not present in the reads. you can trace the clones back to the original reads if necessary. To do this, follow the instructions below: First, run the analysis with these additional parameters:
Then, export alignments from the .vdjca file generated by the above command:
In the Let me know if it helps. |
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So, the R2 reads for 10x are in reverse complement orientation, as shown in the image.
However, the sequences of CDR3 and other regions in MiXCR output are presented in the direct orientation of the coding sequence.
By reverse complementing R2 from your file, we can observe the sequences as follows: