Question: Can I change the sequencing read length of R1N and R2N?
Answer: The final configuration of a single cell ATAC library is the following:
R1N and R2N sequencing reads will capture the DNA insert. These reads will be mapped back to the reference genome and used for peak calling. It is possible to change the lengths of these reads to accommodate different sequencing kit configurations.
Varying sequencing lengths have the potential to affect output metrics. To investigate this, a dataset was trimmed to various read lengths and re-ran on Cell Ranger ATAC. The output summaries are shown below.
In conclusion, the change in cells detected, median unique fragments and mapping rates is minimal when altering the length of R1N and R2N reads.
Note that Cell Ranger ATAC supports read lengths from 30-100bp. Fragments shorter than 30bp are too ambiguous to map, and will cause the software run to fail.
Product: Single Cell ATAC