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Old 04-16-2013, 11:35 AM   #1
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Default sequence read identifiers

Hi all,
We are doing some whole genome on a solid 5500 machine and using all 12 lanes for each sample. My current plan is to align each lane individually, then merge the aligned files together to use in my downstream analysis. My question is regarding the individual sequence read Ids given by the machine. I know that on each lane of the machine, each read has a unique ID, but is that true also for each lane. So for example, if I have read ID of 100_1000_1011, will the be on all lanes of the machine? If so, after I merge everything together, will downstream programs mark these duplicated read names in some way and cause problems for me?
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Old 04-16-2013, 12:18 PM   #2
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Default sequence read identifiers

On Illumina flow cells, the read ID's include the lane number, I'm not sure about SOLID.
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sequence read ids

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