ATAC-seq analysis
1 answer
Please read the manual. https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard
Coordinate-sorted is preferred, here, and in most situations.
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I am using Picard MarkDuplicates to remove the PCR reads, should I give input as a name sorted bam file?