Request for Assistance with 10x 5' V3 VDJ Data Processing in mixcr v4.7.0 #2050
Description
Dear MiLaboratories Support Team,
I hope this message finds you well.
My team and I are currently using mixcr v4.7.0 to process 10x Genomics 5' V3 VDJ sequencing data. We greatly appreciate the power and accuracy of mixcr for immune repertoire analysis and rely on it to generate high-quality AIRR-compliant results.
However, we’ve encountered a compatibility issue: the current stable release (v4.7.0) only includes presets for 10x 5' V2, and does not support the 5' V3 chemistry we are using. We noticed that support for 5' V3 appears to be present in the development version of mixcr, but we were unable to successfully compile it from source. Additionally, attempts to manually reconstruct the command-line workflow based on the V3 preset have failed—specifically, we run into errors during the second round of mitools consensus, where certain required parameters cannot be passed through the current interface.
Given the importance of accurate V(D)J reconstruction for our downstream analysis (including clonotype tracking and AIRR-compliant export), we are eager to resolve this as soon as possible. We would be very grateful for any of the following forms of support:
An official release (or beta) of mixcr that includes the 10x 5' V3 preset;
Guidance on successfully building the development version with V3 support;
Or a recommended set of command-line parameters that replicate the V3 preset behavior in v4.7.0.
Thank you very much for your time and assistance. We truly value your tool and look forward to your reply.