I have a question related to library prep of genomic DNA (*C.elegans*)
prior to whole genome sequencing using Illumina platform.
With previous samples, my lab had used fragmented DNA of size range 100-250
bp before sending it for sequencing. However, the Bioanalyzer results gave
us an unwanted DNA smear at 90 bp region which we presumed were
adapter-dimers. We had then performed gel extraction/purification for a
second time before sequencing.
To avoid that again with our new samples, we thought it would be better to
use fragmented DNA of the size range 300-600 bp.
- What difference, if any, will this make in any aspect (e.g.: number of
reads for each base)?
- Will this affect the amount of coverage as compared to before?