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Old 07-05-2013, 05:39 AM   #1
HelenaSC
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Location: Spain

Join Date: Jun 2013
Posts: 21
Default Newbie question: low cluster density on MiSeq (Chip-Seq pool)

Hi all,

I'm new on this and it seems that's we have some problem with cluster density on MiSeq. We have just run a pool of 2 libraries (from Chip-seq ) , 56 cycles and we are getting very bad results:

* Q-score all cycles: 0.1G, 82%
* Cluster density: 471K/mm2
*Clustering passing filter: 20%

I think that i made some mistake in the calculations preparing the pool of quantified libraries at the time of adding NaOH, but I'm not sure...

I have attached a file with the basic calulations. Anyone could have a look and let me know if I shouldn't have diluted the samples so much?We choose 11pM for final concentration of the pool...was it correct or should we have choosed 11pM for each sample?

Thanks a lot in advance!
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File Type: jpg Chipseq results.jpg (54.7 KB, 75 views)
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