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Recommended pipeline for Cut&Run

Hi,

I have a paired end data from Cut&Run, and I'm about to analyse the data using the pipeline listed in this paper:

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1802-4#Sec8

However, I didn't understand the the way that they trim the data and I couldn't find any informative post or articles that explain the parameters that they used to analyse cut&Run data. Can anyone help me with the pipeline and the list of recommended tools to analyse cut&run data.

Thanks,

Muna

pipeline
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updated by drosophila2021 • drosophila2021 • written by munaj86 • munaj86

A: CUT&RUN analysis pipeline

Some people use bowtie2 with --dovetail option for overlapping reads of very short fragments but I doubt it makes a difference on the big picture.

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written by ATpoint ATpoint

Hi Muna,

Did you get any help regarding this? I am also trying to analyse my CUT&RUN data. I have tried following step by step (not using the cutruntools, but following each step for trimming, alignment, etc and got stuck after alignment...I have then tried "installing" everything to use he cutruntools and got stuck again...)

Thank you!

Kind regards,

Nadia

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written by drosophila2021 • drosophila2021

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