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bam file for bap2 input #38

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yuxia9999 opened this issue Apr 26, 2023 · 2 comments
Open

bam file for bap2 input #38

yuxia9999 opened this issue Apr 26, 2023 · 2 comments

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@yuxia9999
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Hi,
Does the bam file for bap2 input require the reads been duplicates marked, e.g., using Picard to mark the dups but not remove dups? What if I don't run mark dup, the bap2 process will generate some issues, e.g., the jaccard index computations will be too much off?
Thanks a lot!
Yu
@caleblareau
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Nope! there will be duplicate mark / removed during the execution of the basic pipeline

@yuxia9999
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Got it. Thanks for the quick response!

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@caleblareau @yuxia9999