Taq DP is very well known to induce Indels and single base substitutions etc.
So if any polymorphism or genetic variation detected later on, through any NGS platform, what makes us sure that these are not indeed induced and amplified blindly by the Taq polymerase during the library prep steps prior to NGS run.
It depends on what kind of seq analysis you are going to perform. If you want to detect variants, it is better to use a maximum amount of input DNA, which will result in minimum of pcr cycles required for library amplification (or none). Variant analysis also requires a very high coverage (so it means more reads per sample), which reduces the chances of obtaining false positives. If you are interested in e.g. RNA-seq analysis, then random genome variations are acceptable.
if your input options do not allow a PCR-free library, you may want to consider duplicates of your samples if you have enough starting material. In that way you can compare the two duplicates post PCR and eliminate any variation you cannot find in both of them.
You can try using any Polymerase which has less bias for GC regions and has low error rates. All the NGS kits available these days include high performing polymeraseses. We have used a Taq from Kapa biosystems and also a Taq from Thermo and they both work well. Kapa Biosystems Taq performs much better if you have low input.
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