Question: ChIP-seq workflow help
gravatar for wanglp13
19 months ago by
wanglp1310 wrote:


I am a rookie of processing ChIP-seq data, I get a dataset which is about neuroblastoma. To get the effect of N-myc to histone modification, we knockdown N-myc gene in neuroblastoma cell line, untreated neuroblastoma cell line as control.

About H3K4me3/H3K27me3/H3K36me3/H3K9ac initialfiles. I have run MACS2 calling peak with default settings,I got the peak information in files of .bed、.xls、.narrowPeak.

Next,I think i am going to get the position,maybe promoter information,downstream genes. However,I don't know how to do exactly, can someone help?

It would be more nice if you tell me the software to be used.

Thank you very much!

workflow chip-seq • 545 views
ADD COMMENTlink modified 19 months ago by Jennifer Hillman Jackson25k • written 19 months ago by wanglp1310
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Tools in the group Operate on Genomic Intervals can be used for this type of data reduction.

Also please see the tutorials here. Several cover ChIP-seq analysis:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 19 months ago by Jennifer Hillman Jackson25k

Oh,yes. Thank you very much.

ADD REPLYlink written 19 months ago by wanglp1310
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