Question: Using UCSC to Visualize MACs Peak Calling Output
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gravatar for areyoujokingme
4.0 years ago by
United States
areyoujokingme60 wrote:

I am new to bioinformatics and do not know how to retrieve "standard results" from ENCODE and how to visualize that in the UCSC Genome Browser, and then how to visualize User Track based on the BED regions MACs identified as peaks. Here is the result I'm currently getting:

And here are the BED regions MACs gave me back.

_peaks.bed

chr10    69643931    69644105    filePeaks_H3K4M3_peak_1    8.99637
chr15    34330532    34330731    filePeaks_H3K4M3_peak_2    5.01195
chr17    46102870    46103035    filePeaks_H3K4M3_peak_3    3.77451
chr3    195848332    195848497    filePeaks_H3K4M3_peak_4    3.45588

 

_summits.bed

chr10    69644063    69644064    filePeaks_H3K4M3_peak_1    8.99637
chr15    34330646    34330647    filePeaks_H3K4M3_peak_2    5.01195
chr17    46102894    46102895    filePeaks_H3K4M3_peak_3    3.77451
chr3    195848448    195848449    filePeaks_H3K4M3_peak_4    3.45588

 

What oh what am I not doing/doing incorrectly?

chip-seq software error • 1.9k views
ADD COMMENTlink modified 4.0 years ago by RamRS21k • written 4.0 years ago by areyoujokingme60
0
gravatar for RamRS
4.0 years ago by
RamRS21k
Houston, TX
RamRS21k wrote:

BED files supplied to the genome browser with a numeric value for intensity are shown as shades of gray on the browser. Check out the "score" attribute here: https://genome.ucsc.edu/FAQ/FAQformat.html#format1

ENCODE uses wig and bigwig formats to display peaks. These are stored as actual .bigwig files in the mysql database, and I am not sure how the data translates to peaks internally - you may want to dig deeper into that.

ADD COMMENTlink written 4.0 years ago by RamRS21k
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