ATAC-seq analysis

Question

[SEJAL]

After aligning ATAC-seq paired-end reads, the bam files are to be sorted. Should it be name sorted or position sorted?

[GenoMax]

Name sorting would be essential only if you were converting a BAM to fastq reads or marking duplicates. To visualize the data position sort.

[SEJAL]

I am using Picard MarkDuplicates to remove the PCR reads, should I give input as a name sorted bam file?

Answer 1

[ATpoint]

Please read the manual. https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard

Coordinate-sorted is preferred, here, and in most situations.