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Old 10-31-2015, 08:01 AM   #1
tuncmorova
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Location: Turkey

Join Date: Oct 2015
Posts: 2
Default Finding Overlapping Regions of Chip-Seq results, then visualising it.

Hi,

I am trying to visualise my overlapped chip-seq peak regions which I analysed with Homer mergePeaks function. I have got one venn info file and a "result" file. I would like to use that venn info file then visualise it but when I looked for visualisation libraries or programs, I did not find a method which merits my expectations.

The primary problem is my data is big. ( relatively ). I have 19 datasets in one conditions group and 9 datasets in healthy one. I have read making venn diagram for more than 3 datasets would not be smart on biostar tread.

So far, I have tried DiffBind R library to this but I couldn't have figured out its class structure.

I am trying to find overlapped regions of transcriptional factors that why I wanna know which transcriptional factors sites are most common.

I am python coding and R mediocre.

please dont post me ( Venn/Euler Diagram Of Four Or More Sets and Draw Diagrams For Intersection Between Many Sets threads I have already read them 0192308 times), also if you think homer is not the best tool for finding the overlaps, please feel free to advice others. ( Yes, I do know monkseq)

Thank you very much for your help. I have been dealing this step of my project for a week. So I am very frustrated.

Best regards,

Tunc
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chip-seq analysis, homer, venn diagram, visualize ngs data

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