Viewing TF binding CHIP seq data from ENCODE on IGV

[Varun Gupta]

Hi Everyone,

I am interested in ChIP seq analysis of TF 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 (http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeHaibTfbs).

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 and then provide the coordinates of my gene I am interested in and get a nice output in pdf??

Hope to hear from you soon

Regards
Varun

[Jim Robinson]

Hi,  you can load bigwig files from the command line and output svg or png files, as well as provide coordinates.  Please see the user guide for details.

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[Varun Gupta]

Hi
Is this the thing I should look into??
http://www.broadinstitute.org/software/igv/igvtools_commandline
I will let You know if it is working, else you can guide me further.

Thanks
Varun

[Jim Robinson]

Correction, this is more pertinent for your purpose

http://www.broadinstitute.org/software/igv/batch