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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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Is there a reason why cellranger multi does not support 5'-chemistry CMO libraries? #211

Closed dmalzl closed 1 year ago

dmalzl commented 1 year ago

I recently had to reprocess some datasets containing cell multiplexing oligos and found cellranger multi to be a convenient solution for some of the samples. However, I came to the realisation that this convenience ends with 5'-chemistry data which came as a huge surprise as I find the only difference between 3' and 5' TotalSeq libraries is that we sequence the other side of the mRNA. Is there a deeper reason for cellranger multi not supporting 5'-chemistry librariers?

elehnert10x commented 1 year ago

Thank you for your interest in Cell Ranger. GitHub Issues are not monitored by our support team. Please e-mail support@10xgenomics.com for support with Cell Ranger or visit our documentation site at https://www.10xgenomics.com/support/software/cell-ranger.