Hello:
I am currently using Galaxy to analyze several sets of ChIP-Seq datas, including those published and in house generated from my own sample.
When closely looking at two sets of bigWig file of TF binding data in UCSC genome browser, I surprisingly discovered that two of the transcription factors form well overlapped peaks in the promoter region of several genes.
Now I want to do a heat map ploting for genome wide enriched region in one transcription factor and take a look at that generated from another within the same genome X-axis see if it is also enriched. Ho can I do that?
Is there any other bioinformatic assay I could do to determine the extend of co-occupation of two transcription factors?
Thanks in advance for answering those questions!
Yes, heatmap is also an option. If you are using galaxy then this site is also an option to make plots
https://code.google.com/p/ngsplot/
you can make venn diagram to show common and unique peaks of two transcription factors and could also make a line plot around TSS showing average occupancy of both
I am a wet lab person mostly I do is using the public server of galaxy(main), do you know a galaxy instance out there that runs NGS.plot? Thanks a lot!
Understandable!
How to run it on galaxy is also given there:
just click this link
Thank you! Is this a public instance? Looks like it is a Mt Sinai instance? Could you share the link to this instance?
I am a wet lab person mostly I do is using the public server of galaxy(main), do you know a galaxy instance out there that runs NGS.plot? Thanks a lot!