Minimum Requirements for Read Depth and Read Length of Input Data

[HelloYanming]

Hi,

I want inquire about the minimum requirements for the coverage and read length of input single cell data that you recommend to achieve reliable results?

[jluquette]

Hi @HelloYanming,

We typically target 30X mean coverage, but have had success with coverage as low as 20X. Coverage is a little bit more important for somatic indel calling than somatic SNV calling.

We have only used 151bp paired end Illumina reads for PTA. Some much older MDA experiments used 101bp paired end reads, and I don't see why it wouldn't work for PTA as well. It is important to try to match the read length between the bulk and single cell data so that the bulk can serve as a proper control.

Hope this helps