ChIP-seq peaks
Blokhin, Ilya O
Good afternoon.
Would you please help with one question? I am working at the University of Miami and look to visualize ChIP-seq data GSM393952 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM393952) using UCSC.
I am able to map bed file to hg18; however, I do not manage to see peaks. Any advice would be highly appreciated.
Thanks,
Ilya
Christopher Lee
Hi Ilya,
Thank you for your question about hg18 ChIP-Seq peaks. Is it possible for you to elaborate a little further on your issue? We are unsure of what exactly you are asking. Which file from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM393952 did you map to hg18? Are you able to successfully load the file as a custom track on the browser? When you refer to peaks are you thinking of visualizing signal data instead? Can you also elaborate further on what you mean by "I do not manage to see peaks", are you able to successfully load a custom track but there is no data?
If you perhaps meant signal instead of peaks, maybe you just need to
load the variable step Wiggle file as a custom track:
GSM393952_CD4-HDAC3-vstep.txt.gz. Here is a session with that file
loaded as a custom track:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=chmalee&hgS_otherUserSessionName=hg18GSMWiggle
The top most track is the signal track with data from the GSM393952_CD4-HDAC3-vstep.txt.gz file.
Additionally, anything like screenshots, example files, and steps to reproduce your error would be very useful as well!
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Christopher Lee
UCSC Genomics Institute
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Blokhin, Ilya O
Christopher.
Thanks for such a comprehensive approach. You are right, the track you sent is exactly what I wanted to see.
That's what I did. I took the GSM393952_CD4-HDAC3.bed.gz file, uploaded it as a custom track with a goal to visualize the signal (peaks, or where HDAC3 binds to). I was able to upload it but what I saw was different from what I expected. Please see the attached pdf illustrating my erroneous approach: the uppermost track (User Track) shows binding sites of HDAC3 to MAPT (gene of interest) but there is no difference in the height of peaks.
I cc this letter to our grad student Karolina who is in charge of this project. Karolina, please check the link in Christopher's letter, looks like HDAC3 has the strongest signal near MAPT's promoter, as expected.
Thanks very much again,
Ilya
Sent: Tuesday, September 6, 2016 1:25:05 PM
To: Blokhin, Ilya O
Cc: gen...@soe.ucsc.edu
Subject: Re: [genome] ChIP-seq peaks