Why Do 3' Adapter Sequences Appear in Second-Generation Single-End Sequencing
“Next-generation single-end sequencing” refers to the single-end read strategy employed in next-generation sequencing (NGS) technologies, in contrast to paired-end sequencing approaches. In this method, DNA samples are first fragmented into smaller pieces, and synthetic adapters are ligated to both ends of each fragment to facilitate PCR amplification and subsequent sequencing on the platform.
Causes of 3' Adapter Sequence Appearance:
1. Library Preparation
During the library construction phase, adapters are ligated to both termini of the target DNA or RNA fragments. These adapters enable the fragments to be amplified on flow cell surfaces or magnetic beads and serve as priming sites for the sequencing reaction.
2. Sequencing Read Length
When the sequencing read length exceeds the length of the target insert, the read extends into the 3' adapter region, resulting in the adapter sequence being incorporated into the sequencing output.
3. Data Analysis
Bioinformatics tools are commonly employed to identify and remove adapter sequences from the raw data, as these sequences do not originate from the biological sample and may interfere with downstream analyses.
In summary, the presence of 3' adapter sequences in next-generation single-end sequencing results from the combined effects of library preparation and the sequencing read length. To ensure the accuracy and quality of sequencing data, these adapter sequences must be effectively detected and trimmed during data processing.
MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider.
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