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3 months ago
Zeke
•
0
Hi,
I have narrow peak data obtained from chipseq for a given transcription factor. I would like to know whether the chip peaks are on the promoter regions of a list of genes differentially expressed in a sample.
Are you familiar with R or the command line? Or looking for a web tools?
In R, there's some tools that can do this with minimal work from you like ChIPseeker or ChIPpeakAnno.
On the command line, you can relatively easy generate a promoter list from your genes of interest and the find intersections with bedtools or similar.
I'm not very familiar with web tools for this. This one maybe can accomplish what you need although indirectly (it will annotate your peaks with genes and you will need to filter for your genes of interest). https://meme-suite.org/meme/doc/tgene.html?man_type=web
Yes I am familiar with both. I am currently going through ChIPseeker documentation to understand how to go about it. I wanted to understand if there's another way. Thanks for your reply.