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Old 01-05-2012, 08:20 AM   #1
kjsalimian
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Default Paired end reads of unexpected sizes??

Hi guys,

I have recently performed a ChIP-Seq experiment using the Illumina HiSeq2000 platform, 100 bp-paired end. When I aligned my paired end data to the genome using Bowtie, I get some unexpected results.

My Input library DNA looks like a perfect mononucleosome peak (~155 bp + 125 bp adapators) on the bioanalyzer. However, when I look at a histogram of my aligned reads, I get a distribution of reads that are around 155 bp but I also get a a HUGE peak around 110 bp. I don't see any peak around 110 bp in the library on the bioanalyzer.

Has anyone encountered such a thing or have any idea what might cause it? Possibly the clustering is extremely efficient for these ~110 bp sequences?

Thanks for your help.
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Old 01-05-2012, 09:00 AM   #2
Heisman
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Could you upload the bioanalyzer trace?
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Old 01-05-2012, 09:15 AM   #3
HESmith
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Just a guess: the 110bp peak is from reads where only one of the two ends aligned.
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Old 01-05-2012, 09:28 AM   #4
kjsalimian
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BioA trace attached...
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