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Old 12-01-2014, 12:24 PM   #1
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Location: France

Join Date: Mar 2011
Posts: 2
Default fewer reads after Input library sequencing

I am newbies in this forum and this is my first post. I have recently performed H3K4me3 ChIP librairies preparation with using NEXTflex ChIP-Seq kit to sequencing 18 Immunoprecipitation products (IPs)and 6 inputs as negatives controls.
This sequencing is achieved on 3 Illumina Rapid flow cells with PE 2X50 pb reads. 3 IPs and 1 input have been sequenced in the same lane onto HiSeq 2500 with the new version of HCS 2.2.38 software. After Casava demultiplexing, I have getting 80 to 100 million reads with IP librairies and 30-36 million reads for input librairies. I have used 5% PhiX as a balanced genome for this experience because I have get a good results last time when we used 1% PhiX with the old HCS version.
Can you help me please to understand this result.

Thanks a lot.
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