MNase-Seq fragment size

Question

[Constantine]

Hello Biostars

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:

-SE

-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 ?

Thanks :)

Answer 1

[Devon Ryan]

If you want to split things by subnucleosomal and mono-nucleosome then you absolutely requrie paired-end reads.

Edit: I'll add the PE sequencing is the norm for MNase-seq, since it more reliably allows you to look at nucleosome positioning. Some things, such as the --MNase setting in bamCoverage won't even work with SE data.