I am planning on doing an MNase-Seq experiment and I have some technical questions.
For the analysis I am intending to splitting the files by fragment size to characterize:
- Subnucleosomal occupancy (~80-100 bp fragments)
- Nucleosomal occupancy (~130-150 bp fragments)
Usually MNase-Seq data are paired-end. However, people in our sequencing facility told me that single-end should also do the job. They intend to sequence:
-Each sample at ~200 million reads depth (150 bp reads)
Will the above parameters work for the above analysis I am planning or do I need to go for PE sequencing ?