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Old 07-01-2013, 03:28 AM   #1
ester
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Default PhiX control lane in Hiseq2500

Hello,

I would like to know if you are running phiX in a separate lane to calculate a matrix in HiSeq2500 runs.

And if not, what applications are you running (RNA-Seq, ChIP-seq, exome, etc.) and how are you calculating the matrix for pre/phasing?

Thanks
Ester
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Old 07-01-2013, 03:47 AM   #2
GenoMax
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Do you have a particular kind of sample that you are worried about? Are you referring to a "normal" run on the HiSeq 2500 or rapid mode? Having just two lanes to work with (in rapid mode) it would be expensive to run phiX on one of the lanes but it should be possible to do and to designate it as the "control" lane.

With regular flow cell (8 lane) you can either run phiX in one lane (as a control).

In either case, you can also run a "normal" sample that is expected to have uniform nucleotide distribution and designate that lane as control.

Last edited by GenoMax; 07-01-2013 at 03:49 AM.
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Old 07-01-2013, 03:57 AM   #3
ester
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Thank you for your answer.

I was thinking of regular flow cells (8 lanes). We are worried about chIP-seq or even RNA-seq samples with biases in the nucleotide composition.
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Old 07-01-2013, 04:07 AM   #4
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If you want to be absolutely sure then indeed use a control lane but in general you should not need a control lane with regular ChIP-seq and RNA-seq samples.

You will see some base bias with Illumina sequencing (specially for RNA-seq) in the first 10-15 bases. That is normal. See this thread for background information: http://seqanswers.com/forums/showthread.php?t=11843
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