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Old 04-11-2012, 07:15 AM   #1
aritakum
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Default ChIPSeq: Unusual narrow peaks

HI,
I am looking at some ChIPSeq data that is rather unusual. The forward and reverse reads form deep thin stacks. Their width is mostly just above the read length of 75 bp. The 'peaks' (pseudo-peaks?) are distributed well across the mouse genome. Have any of you see this? What could be the reason? This experiment is investigating transcription factor binding ....


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Jarus
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Old 04-11-2012, 08:02 AM   #2
ffinkernagel
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Hm. Sounds to me like a very low complexity library - I have seen one or two of those, but can only speculate about the reason.
Perhaps very low amounts of input dna with too many PCR cycles?
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Old 04-11-2012, 08:19 AM   #3
ETHANol
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Sounds like a low complexity issue but it would be helpful if you posted some images of what the data looks like.
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Old 04-11-2012, 10:08 AM   #4
aritakum
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Default RE: ChIPSeq: Unusual narrow peaks

Attached is a screen shot of what I typically see through out the genome
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File Type: gif chr7.gif (12.9 KB, 45 views)
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Old 04-11-2012, 10:47 AM   #5
steinmann
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Yes, thats what PCR artifacts from low complexity libraries look like.
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Old 04-11-2012, 10:50 AM   #6
aritakum
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Thank you all. I think its time to get back to re-doing experiment. I guess, Data analysis-wise there is not much to do...
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