Question: ChIP-seq blacklisted regions (mouse)
0
gravatar for Constantine
3.6 years ago by
Constantine220
USA
Constantine220 wrote:

Hello

I have aligned ChIP-Seq data to the mm10 genome, called peaks and now I want to remove the blacklisted regions.

However, the blacklist bed file provided by ENCODE is for the mm9 genome. Would it be sensible to use this file or do you think that co-ordinates might be shifted and ultimately will remove non-blacklisted regions from my datasets?

If not, is there a way to find the actual blacklisted regions for mm10?

In the end, I could align to the mm9 but I prefer using the latest genome annotation

Thank you

 

sequencing chip-seq next-gen • 1.7k views
ADD COMMENTlink modified 3.6 years ago by Chirag Nepal2.2k • written 3.6 years ago by Constantine220
1
gravatar for Chirag Nepal
3.6 years ago by
Chirag Nepal2.2k
Copenhagen
Chirag Nepal2.2k wrote:

Use LiftOver tools from UCSC genome browser and change the coordinates from mm9 to mm10.

 

ADD COMMENTlink written 3.6 years ago by Chirag Nepal2.2k

Thank you..That did the trick ;)

ADD REPLYlink written 3.6 years ago by Constantine220
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