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daler / metaseq

Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data
https://daler.github.io/metaseq
MIT License
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sample snippet for the ChIP signal visualization? #37

Open zhenyisong opened 6 years ago

zhenyisong commented 6 years ago

I want to extract the TNNI3 gene for example, and plot the ChIPseq signal extending from specified upstream region to downstream region. And pile up several other plots including gene body etc. I am struggling to migrate my code to python for the future maintenance.

I read the script <Example 1>. It seems that I have to call other python package( in my case , I have to create a feature object for the TNNI3 gene) to complete the above task and no one-stop solution in the current metaseq package.

Anyway, any suggestions are appreciated. ( I prefer more python way, not using rpy2 as the bridge to call R/bioconductor.)

daler commented 6 years ago

That's correct, metaseq does not know anything about gene locations. You might want to give deepTools a try, since it is better maintained than metaseq. It is also written in Python. However you will still need to know the coordinates of the gene(s) you're interested in.