CUT&RUN analysis pipeline

Question

[pixie@bioinfo]

Hello, My lab has generated data using the CUT&RUN protocol. Unfortunately, Its single-end data. I tried the CUT&RUN tools and the henipipe tool. Both are for paired end data.

Any suggestion how I can analyse these data ? Any idea how to set the parameters in case I use the classical Trimmomatic and bowtie2 ? Any other pipelines to try ?

Thanks and Regards. (Loosing my mind)

Answer 1

[rpolicastro]

You don't need to do anything too special. Trim adapters with your favorite software, align to genome using BWA-MEM or bowtie2, and call peaks using MACS2.

Most of the fancy stuff with CUT&RUN is when you have paired end data. With paired end data you get information on insert/fragment size, which can be used to infer nucleosomal and subnucleosomal fragment, which in turn lets you guess whether afragment was from nucleosome protection or TF binding.

[schowdhury8950]

rpolicastro Hi, could you please help me understand which type of control is most appropriate for peak calling in CUT&RUN using MACS2? While input DNA is commonly used as a control in ChIP-seq, would IgG be a more suitable control for CUT&RUN?