Gene locations do not match
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Entering edit mode
6 months ago
rbravos87 • 0

Hi all,

it is the first time I am doing ChIPseq (I used Galaxy). I obtained a list of enriched genes and their locations.

But when I want to see (graphically) the reads, I use the BAM files in IGV. The point is that the location of the given genes by Galaxy and the location of the genes in IGV is a little bit different. I always used "mm10" as genome reference

For example, for Ccne1 ChIPseeker gave me Chr7: 38,084,915 - 38,085,196. However in IGV it appears in 38,097,984 - 38,107,490.

I guess that this can affect my interpretation.

Any suggestion?? I really would appreciate it!! Thanks in advance.

ChIP-Seq • 368 views
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Entering edit mode
3 months ago
gglim ▴ 80

I didn't find location in your answer for Ccne1

38,084,915 - 38,085,196

May you show your code for annotation part i.e.

annotatePeak(...) of ChIPseeker

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