Question: CUT&RUN analysis pipeline
0
gravatar for pixie@bioinfo
5 weeks ago by
pixie@bioinfo1.4k
Université Paris, Saclay
pixie@bioinfo1.4k wrote:

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)

sequencing alignment • 149 views
ADD COMMENTlink modified 5 weeks ago by rpolicastro2.3k • written 5 weeks ago by pixie@bioinfo1.4k
0
gravatar for rpolicastro
5 weeks ago by
rpolicastro2.3k
rpolicastro2.3k wrote:

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.

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by rpolicastro2.3k
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