Viewing Tf Binding Chip Seq Data From Encode On Igv

Question

[Varun Gupta]

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 (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 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

Regards

Varun

[Devon Ryan]

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

Answer 1

[Sukhi Singh]

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

https://bitbucket.org/dalloliogm/ucsc-fetch/overview