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Old 02-06-2013, 02:57 PM   #1
byou678
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Arrow Do we need two DIFFERENT adapters to generate Pair-end Reads ?

Hi All,

I am wondering: Must we have at least two adapters to generate Pair-end Reads(Take Illumina Platform for example) ?
I am also not sure about using other Platforms.

I found this tread in SEQanswers below
http://seqanswers.com/forums/showthread.php?t=17939

"vinay052003" said " I am not sure about other technilogies, but for Illumina 5' end sequencing cycle starts right from the start (5' end) of the actual sequence. So adapters sequence contamination in the final read would be only on 3' end. " Do you agree?

Thanks a lot for any response!!

Last edited by byou678; 02-07-2013 at 07:04 AM.
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Old 02-06-2013, 05:40 PM   #2
rflrob
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Not sure if Bioinformatics is the right place for this question, given that there's an Illumina section, but I'm pretty sure both ends do need an adapter to do the bridge PCR. If you're doing anything like the standard library prep, however, that should get it onto both ends.

As far as the adapter sequence, you conceivably could get adapter sequence at the beginning of each of the paired-ends of the reads. What won't happen, except in vanishingly rare cases, is that the forward read will start in the adapter sequence and then read into the adapter sequence on the other end of the fragment. It's possible, I suppose, but only if your fragments are really small, and at that point, I'd be concerned about other problems in your library prep.
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Old 02-07-2013, 12:25 AM   #3
dpryan
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I've seen adapter contamination at either end of reads. This can be a particular problem in RRBS, where the read length can be greater than the insert (and the reduced base-space makes any adapter contamination a real problem). I adapter and quality trim from both ends of reads prior to doing anything (regardless of the type of data).
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Old 02-07-2013, 07:03 AM   #4
byou678
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Quote:
Originally Posted by rflrob View Post
Not sure if Bioinformatics is the right place for this question, given that there's an Illumina section, but I'm pretty sure both ends do need an adapter to do the bridge PCR. If you're doing anything like the standard library prep, however, that should get it onto both ends.

As far as the adapter sequence, you conceivably could get adapter sequence at the beginning of each of the paired-ends of the reads. What won't happen, except in vanishingly rare cases, is that the forward read will start in the adapter sequence and then read into the adapter sequence on the other end of the fragment. It's possible, I suppose, but only if your fragments are really small, and at that point, I'd be concerned about other problems in your library prep.
Thanks for the reply!!

Futhur, must we have at least two DIFFERENT adapters to generate Pair-end Reads(Take Illumina Platform for example) ?
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Old 02-07-2013, 08:05 AM   #5
kwaraska
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No-using the TruSeq adapter format they are double stranded (Y-adapters)so one side is the forward read and the other is a reverse read on the same strand.

For example-the forward read is the "top" of the Y on one side, but they way the adapters are ligated, that sequence will be on the "bottom" of the other end.
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