File: index.mapped.bam

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This file is generated after mapping to the reference genome and selecting high-quality primary alignments with a mapping quality score of > 30. It is generated after alignment but before barcode correction or cell calling. It maps all the barcodes and is index-specific, meaning for only one tube.

A .bam file is a binary version of a sequence alignment map (SAM). For more information on these formats, refer to this PDF. To visualize these files, use tools like IGV

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