ATAC-seq quality control

[Kath]

Hello,

I am analysing ATAC-seq data for the first time and am wondering what typical values are for:

Total number of reads
Duplication rate
Percentage of reads uniquely mapping
Percentage of reads that map to protein-coding genes

Once I've finished mapping I'll post the values I get.

Also, what metrics do you take into account when assessing the quality of your ATAC-seq data?

Many thanks in advance,

Kath

[atpoint]

- the total number of reads depends on the platform you sequence on. on a miseq it should be about 25mio per flowcell, on a nextseq500 it can be up to 400mio. instead of total read numbers, better check if the alignment rate is sufficiently high. also keep in mind that many reads will map to the mitochondrial genome, as the MT chromosome is also transposed during sample preparation. primary cells typically have a smaller fraction of MT than (tumor) cell lines. values between 50-80% of mt reads are not unusual.