CUT&RUN analysis pipeline
Entering edit mode
3.0 years ago
pixie@bioinfo ★ 1.5k

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)

alignment sequencing • 1.4k views
Entering edit mode
2.9 years ago

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.


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