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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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Selecting primary alignment in duplicate reads #213

Closed kwcurrin closed 8 months ago

kwcurrin commented 1 year ago

Hello,

In cellranger-arc for ATAC-seq, how is the primary alignment chosen out of a group of duplicates? Is it random? Or is it based on base quality like picard or mapping quality like samtools? Or some other method? Where could I find relevant code in the cellranger-arc instllation?

Thanks,

Kevin

elehnert10x commented 8 months 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.