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Old 02-14-2011, 12:30 AM   #1
khb
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Location: Oslo

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Question Long peaks

Hi
I've done a chip-seq experiment, and used the program MACS. When I look at the peaks in UCSC genome browser, the peaks are very long, see pdf file for example from mitochondrial chromosome. Is this peak likely too bee a real peak?
We believe that it will not bind direct to a DNA but likely as a part of a complex.
Thanks for all replies
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File Type: pdf hgt_genome_4841_8f3860.pdf (37.5 KB, 50 views)
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Old 02-14-2011, 07:20 AM   #2
csoong
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Never had any chip-seq experience. But are the peaks directly related to coverage? since chip-seq only selects a portion of the genome having high coverage (hence seeing higher peaks) is expected, right?

By the way, what were you expecting? And please forgive me if I totally misunderstood your question.
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Old 02-14-2011, 11:23 AM   #3
danielr
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If it's on the mitochondrial chromosome, assume it's not real. You pick up things there because it doesn't have the same copy number as the nuclear chromosomes.
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Old 02-15-2011, 05:04 AM   #4
epigen
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The length of your peaks depends on the value for the --bw parameter you give MACS. It should be the same as the fragment size. The higher the value, the longer the peaks.
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Old 02-16-2011, 12:36 AM   #5
mudshark
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looks weird.

what was your experimental layout, did you use a control/input sample?

is your chip target supposed to enter the mitochondria, is it a mitochondrial protein, is your result plausible?

did you try any other peak caller, SISSR, Quest?
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Old 02-16-2011, 01:36 AM   #6
mapper
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I have also seen very large peaks with MACS ...you can either use peak splitter program...or you can try sissr which will give very sharp peaks....
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