Question regarding read depth for control samples in ChiPseq

[linelieblein]

I have earlier used Genrich to analyse our ATACseq data and I am now in the process of preparing samples to analyse histone marks in different tissues of salmon. I have a good idea of the number of reads I need for the immunoprecipitated samples , but I am not sure what read depth I need for the input control samples.

Since I am going to use Genrich to analyse the native chip samples, do you have any recommendation concerning the sequencing depth of the input control samples. I am asking because I think the different peak callers might have different preferences for the amount of reads from the control samples versus the experimental samples.

Thanks in advance, Best, Line Lieblein Røsæg

[jsh58]

Thanks for the question. Ideally, the control samples would be sequenced to the same depth as the experimental samples. However, as described in the README:

Note that control pileups are scaled to match the experimental, based on the total sequence information in each.

Therefore, variability in sequencing depth is accounted for by Genrich. Its verbose output will indicate the scaling factor.