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Old 09-20-2013, 06:58 AM   #1
dgasx8
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Location: Italy

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Default nextera exome

Hi, I am planning to sequence
a series of human tumors by the nextera rapid capture expanded exome kit.

Using the HiSeq1000, to obtain 100x coverage, the "coverage calculator for Illumina Sequencin systems" recommends loading pools of 6 samples/lane (with 200 cycles).

But I was told that it is less expensive to make 12-samples enrichment pools and load them twice (12samples/lane, 2 lanes).

Can anybody confirm this or give me other suggestions?
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Old 09-23-2013, 12:51 AM   #2
weigrc
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Default

This kit its exome target region is ~62 Mb.

With HiSeq PE_100 sequencing, in order to get 100X coverage per sample, need to do sequencing in a basis of 6 samples per lane. (~35Gb / 62 Mb / 6 samples).

And Illumina recommends each capture reaction its capacity can process maximum 12 samples.

Therefore, as your plan, the most cost-efficient way is to run each capture pool with 2 PE_100 sequencing lanes.
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