ATACseq libraries differ in each run

Question

[rahel14350]

Dear all,

I did some ATACseq last year and we wanted to repeat it this year using the same isolation and preparation kits but the libraries looks so different. Is there anybody had the same experience and if you advice to do the sequencing based on this libraries?

Many thanks in advance, Rahel

[ATpoint]

The first two panels are fine and as expected, the last two have the expected peak at 200bp but are somewhat missing the banding pattern that should follow the peak at 200bp. Quite some large fragments in the last two. I had that sometimes in my samples and never found out why but sequencing was always ok if memory serves. I would simply submit them for a shallow sequencing, so try to spike them in in any run and then check the sequencing data, these Bioanalyzer tracks sometimes look odd, especially if the early samples had large fragments which then partially block or slow down transition of the later samples through the capillaries, I would not overinterpret them.

[rahel14350]

Thanks a lot for your reply.