I have the Chip Peak calling sequence data for a gene, and I need to find out Transcription factor binding site at the promoter region of a gene. I have selected the EMSA to find out whether to check the transcription is binding to the promoter region..Since I have many gene, is there any way to use the chip peak calling sequence to find out the Transcription factor binding site..
Thanks in Advance..
Hi Jayalakshmi, what kind of peak calling file do you have? I assume you have a .narrowPeak, or a .bed file. You can use the Intergrated Genomics Viewer to look at the transcription factor 'peak presence' at a specific genomic location.
http://software.broadinstitute.org/software/igv/home
Just remember that this will not give you the TF binding intensity/enrichment, but just the mere presence of a peak.
All the best.
Thank you for your kind reply, Sir. I am not sure about it but I guess its is bed file and I will look into genomic viewer to use.
You're welcome Jayalakshmi Thiruppathi let me know how it goes
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