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)
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pixie@bioinfo
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.
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?
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