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Old 10-24-2013, 01:29 PM   #1
seqgirl123
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Default flowcell help

Can a single end library be sequenced on a paired end flowcell? Or is it a paired end library can be sequenced on a single end flowcell?

For the dual index libraries, Illumina says one can "perform dual index single end sequencing on a paired end flowcell containing paired end libraries" with the HiSeq 2500. I am not clear on the wording. Do they mean, that your PE libraries with dual indexes can be run on a SE flow cell??
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Old 10-24-2013, 02:55 PM   #2
GW_OK
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SE's can go on PE's, PE *cannot* go on SE.

Not sure about dual indices, but it would make sense that you could do a dual indexed single read on a PE flowcell, but aren't dual indixed libraries PE in nature intrinsically?

Does illumina still make SE library oligos?
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Old 11-13-2013, 07:17 AM   #3
HeinKey
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Illumina mentioned you can sequence PE libraries on a PE flow cell, in SE mode. So sequencing only read one.
SE dual indexing is possible, also on a PE flow cell. This is because the second index starts from a newly hybridized index primer in SE mode. You need the SR dual indexing kit for this!
In PE mode the second index is sequenced using the grafted P5 oligo which is extended first for 7 (dark) cycles. This last step does not work on a SE flow cell.
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Old 11-13-2013, 10:24 AM   #4
kmcarr
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Quote:
Originally Posted by seqgirl123 View Post
Can a single end library be sequenced on a paired end flowcell? Or is it a paired end library can be sequenced on a single end flowcell?

For the dual index libraries, Illumina says one can "perform dual index single end sequencing on a paired end flowcell containing paired end libraries" with the HiSeq 2500. I am not clear on the wording. Do they mean, that your PE libraries with dual indexes can be run on a SE flow cell??
Seqgirl,

[Assuming your are talking about standard Illumina libraries]

There really is no such thing (anymore) as a "single end library". Illumina did away with the distinction between single-end and paired-end libraries with the introduction of TruSeq.

TruSeq libraries are paired-end by default and may be sequenced equally well using either an Single Read (SR) or Paired End (PE) Cluster Generation kits (flow cells). This also applies to their prep kits which generate Dual Indexed libraries. But be aware that on the HiSeq 2000 or HiSeq 2500 in High Output Mode you will need to purchase an additional primer kit if you want to run Dual indexed libraries with a SR Cluster Generation kit. Illumina has a compatibility matrix somewhere indicating when you do and do not need the additional primer kit but I can't find it now. Ask your FAS or Account Manager if they can provide it to you.
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Old 11-14-2013, 04:49 AM   #5
rajasereddy
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You can't use SR flow cell for PE read either it is dual index or single index.
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