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Can't calculate duplicates from flag in BAM output of Optimus, Multiome, and Slideseq #1115

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ekiernan opened this issue Nov 2, 2023 · 2 comments
Open

Can't calculate duplicates from flag in BAM output of Optimus, Multiome, and Slideseq #1115

ekiernan opened this issue Nov 2, 2023 · 2 comments

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@ekiernan
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ekiernan commented Nov 2, 2023 •
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The tool we use in for calculating optical/technical duplicate reads from the STARsolo BAMs requires a flag of 1024, which is captured in the BAM_FDUP attribute of the htslib.sam.h library used by TagSort. STARSolo does not currently output this for duplicate reads.

We can explore an alternative solution for duplicate calculations.
@ekiernan
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ekiernan commented Dec 6, 2023

We are still exploring options for this. Documentation has been updated to reflect that the TagSort metric is not calculated for the Optimus workflow. https://broadinstitute.github.io/warp/docs/Pipelines/Optimus_Pipeline/Loom_schema

@jessicaway
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This is still an issue

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@jessicaway @ekiernan