hi there,
can anybody explain me, why i become in pcr 300 bp fragments, but cut out in the gel after ligation of the adapters 400-450 bp?
in NEBNext sample prep i see the problem and for the truseq protocol illumina gives warning for this:
"Cutting a band between 400–500 bp will result in an insert size of approximately 300–400 bp, accounting for the size of the adapters. Adapters add approximately 120 bp to each fragment. The sequencing read length should be considered when cutting fragment sizes. Sequencing reads that over‐reach into the adapter will cause chimeric reads, unalignable to the reference sequence."
is there a name for this? is the effect only for ds DNA Fragments?
can anybody explain me, why i become in pcr 300 bp fragments, but cut out in the gel after ligation of the adapters 400-450 bp?
in NEBNext sample prep i see the problem and for the truseq protocol illumina gives warning for this:
"Cutting a band between 400–500 bp will result in an insert size of approximately 300–400 bp, accounting for the size of the adapters. Adapters add approximately 120 bp to each fragment. The sequencing read length should be considered when cutting fragment sizes. Sequencing reads that over‐reach into the adapter will cause chimeric reads, unalignable to the reference sequence."
is there a name for this? is the effect only for ds DNA Fragments?
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