Question: Viewing Tf Binding Chip Seq Data From Encode On Igv
gravatar for Varun Gupta
6.6 years ago by
Varun Gupta1.2k
United States
Varun Gupta1.2k wrote:

Hi Everyone,

I am interested in ChIP seq analysis of TF(transcription factors) for Ribosomal Protein Genes for some cell lines(eg A549,GM12872 etc). As a start I am using Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB (

What I want to do:

For 1 particular gene let's say RPL3, for 1 cell line lets say A549, I am interested in getting their bigwig graph representation on IGV for different Transcription Factors(like YY1,MAX,GATA3 etc).

Is their a way to do this on command line with IGV tools and then save the results on the pdf file. I would like to adjust track height also.

Since there would be a lot of TF's, loading every bigwig file(one for each TF) would make IGV slower I guess. So Is there a way on command line where I can input these bigwig file or may be .bam files and then provide the coordinates of my gene I am interested in and get a nice output in pdf for all the TF's bam/bigwig files??

Hope to hear from you soon



igv • 3.2k views
ADD COMMENTlink modified 6.4 years ago by Sukhdeep Singh10k • written 6.6 years ago by Varun Gupta1.2k

Is there a reason you want to do this in IGV rather than just using Gviz?

ADD REPLYlink written 6.5 years ago by Devon Ryan97k
gravatar for Sukhdeep Singh
6.4 years ago by
Sukhdeep Singh10k wrote:

You can use Giovanni's script for this purpose (uses UCSC instead of IGV), very efficient and more extensive than IGV.

ADD COMMENTlink written 6.4 years ago by Sukhdeep Singh10k
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