In a metagenomic library profile desired size is 450-550bp,getting unwanted fragments which is causing failure of the library or it is difficult to get the desired data after sequencing.
Its actually amplicon library prep.
And you should be checking your PCR protocol for why you are getting longer amplicons in the first place. Second, the cleaning protocol should be optimized.
Generally, column-based PCR cleanup protocols / or bead-based purification are not that efficient in removing short bases in the samples. I suggest doing a gel extraction of PCR product to select the desired size, before starting with library preparation. During library preparation, you can do bead-based purification as suggested by the manufacturer. However, starting material is very crucial in the NGS. We follow this in our lab, and we always get a good library with desired sequencing data. Regards
Venkat
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