Plot read density across a normalized gene model for its each exon/intron length
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2.0 years ago
kashiff007 ★ 1.6k

I know there are several tool which can plot ChIP-seq score based on annotation file (GTF/GFF3/BED), but Is there any standard tools in R/python which can plot and normalize to gene model for its each exon/intron length?

I am looking for the following output:

enter image description here

Here score from each exon/intron are normalized to its length.

ChIP-Seq deeptools next-gen R python • 853 views
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BTW, where and how did you get this representation?

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2.0 years ago
yusuf ▴ 60

1 - tool - http://www.iam.u-tokyo.ac.jp/nakatolab/softwares/drompa/index.html 2 - by SGA files https://ccg.epfl.ch//chipseq/doc/chipseq_tech.php 3 - paper - Wessels HH, Hirsekorn A, Ohler U, Mukherjee N. (2015) Identifying RBP Targets with RIP-seq. Methods Mol Biol 1358:141-52

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Thanks but unfortunately none of the above work for gene model normalization.

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2.0 years ago
benformatics ★ 2.6k

You could try the Guitar package.

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