Question: Plot read density across a normalized gene model for its each exon/intron length
2
gravatar for kashiff007
9 months ago by
kashiff007130
Cologne
kashiff007130 wrote:

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.

ADD COMMENTlink modified 9 months ago by benformatics1.9k • written 9 months ago by kashiff007130

BTW, where and how did you get this representation?

ADD REPLYlink written 9 months ago by Nitin Narwade450
0
gravatar for yusuf
9 months ago by
yusuf50
Norway INN
yusuf50 wrote:

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

ADD COMMENTlink written 9 months ago by yusuf50

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

ADD REPLYlink written 9 months ago by kashiff007130
0
gravatar for benformatics
9 months ago by
benformatics1.9k
ETH Zurich
benformatics1.9k wrote:

You could try the Guitar package.

ADD COMMENTlink written 9 months ago by benformatics1.9k
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