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.