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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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Is gex_possorted_bam.bam deduplicated ? #154

Closed plbngl closed 8 months ago

plbngl commented 2 years ago

Hi! I am using cellranger arc 2.0 and need to use the .possorted.bam files for allelic quantification and wanted to remove PCR duplicate reads. For the gex_possorted_bam.bam I have a doubt regarding UMI: I understood that reads coming from the same UMI barcode and cell barcode and mapping to the same gene are counted only once in the count matrix, but I did not understand if the BAM file is already filtered for duplicated reads with same cell and molecule barcode and mapping to the same position. If not, how do I filter it? Thank you!!

Paola

plbngl commented 2 years ago

Any comment on how to remove PCR duplicates from a 10x gene expression bam file? Thanks!!