Question

Chipseq visualization how to draw the figure

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3.3 years ago

Binghong ▴ 20

Dose anybody know how to draw the figure using Chpseq data？ Any guidance would be appreciated ！ enter image description here (the figure is from The Histone Lysine Demethylase JMJD3/KDM6B Is Recruited to p53 Bound Promoters and Enhancer Elements in a p53 Dependent Manner)

peaks Chipseq • 1.3k views

ADD COMMENT • link 3.3 years ago by Binghong ▴ 20

score 2 · Answer 1 · 2021-08-12

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3.3 years ago

Chirag Nepal ★ 2.4k

This looks like a UCSC genome browser screen shot. To do this 1) Convert your mapped BAM file into bigwig format. Use deeptools to convert bigwig file 2) Then upload your wig file on UCSC genome browser and then you can get such plots.

ADD COMMENT • link 3.3 years ago by Chirag Nepal ★ 2.4k

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Yeah, the overall appearance looks like UCSC. If you want to automate things starting from bigwig files you might be interested in https://github.com/PoisonAlien/trackplot which does these kinds of coverage plots, fully in R with options to highlight and customize. trackplot: Fast and minimal dependency standalone R script to generate IGV style locus tracks from bigWig files

ADD REPLY • link 3.3 years ago by ATpoint 85k

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thanks! it helps me a lot

ADD REPLY • link 3.3 years ago by Binghong ▴ 20

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thanks! it helps me a lot

ADD REPLY • link 3.3 years ago by Binghong ▴ 20