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Old 11-06-2013, 02:03 PM   #1
Genohub
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Default Ligation Biases during library construction

Has anyone else experienced this base composition bias during ligation? Check out figures 1 & 2:


Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes

http://www.plosone.org/article/info%...l.pone.0078575

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Old 11-07-2013, 05:19 AM   #2
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I have not looked at this but they use a library prep method where the dNTPs are not removed before A-tailing. This reminds me of a poster from Life where dNTPs where shown to cause similar bias against inserts starting with T/C:

http://www3.appliedbiosystems.com/cm...cms_091610.pdf
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Old 11-07-2013, 05:42 AM   #3
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Interesting poster. This paper also compares blunt ended vs. AT ligation. It would nice to see whether any of the combined End Repair / Adenylation steps that use just a polymerase to A-tail (and have to deal with a full assortment of dNTPS, rather than just dA) are also introducing bias or just reducing preparation efficiency.

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adapter composition bias, ligation bias

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