Hello,
I am planning a targeted resequencing experiment using the Illumina TruSight Cancer panel, which claims an average insert size of 300bp. Illumina people recommend MiSeq 2x150 runs but, as in my sequencing service MiSeq 2x250 runs are just 8% more expensive than MiSeq 2x150 runs, I wonder if it wouldn't be worth to use MiSeq 2x250 runs. I understand that many pair reads will overlap, but I still think I will gain a considerable amount of coverage. I'd like to find medium (1-50bp) insertions and deletions and hope that longer reads will help me to align them properly. Is this correct? Are any quality differences between those chemistries that I should take into acount? Any appreciation is welcome!
I am planning a targeted resequencing experiment using the Illumina TruSight Cancer panel, which claims an average insert size of 300bp. Illumina people recommend MiSeq 2x150 runs but, as in my sequencing service MiSeq 2x250 runs are just 8% more expensive than MiSeq 2x150 runs, I wonder if it wouldn't be worth to use MiSeq 2x250 runs. I understand that many pair reads will overlap, but I still think I will gain a considerable amount of coverage. I'd like to find medium (1-50bp) insertions and deletions and hope that longer reads will help me to align them properly. Is this correct? Are any quality differences between those chemistries that I should take into acount? Any appreciation is welcome!
Comment