ATAC-seq mode

[MERobinson]

Hi,

Could you maybe add an explanation of what exactly the ATACseq mode (-A flag) is doing differently to DNase mode? Also should the input BAMs for ATACseq mode be Tn5 shifted or not?

Thanks

[pc297]

Hi, the -A flag results in the reference, not the bam file, being shifted, and by -5bp for the + strand and +4bp for the minus strand (which effectively amounts to shifting the bam file by +5bp/+ -4bp/- as described in the Buenrostro paper). So the bam file does not need to be shifted.