I am planning some experiments that involve sequencing products that have a standard adaptor sequence at the start.
Now I know that the cluster identification occurs using bases 1-5 so I have thought about using a NNNNN after the sequencing primer. This should ensure that clusters are identified correctly.
However, for bases 6..15 all clusters have the same base. This will produce a single colour per flow, and there will potentially be optical effects due to saturation. Now, I don't really care about these bases, I am only interested in the genomic bases after the adaptor. So my question is: will the later bases be sequenced OK given that the early bases may have these problems?
Also, what will happen for the paired end read if that also has low complexity bases at the start? Since the cluster identification happens during the first read, the effect should be the same?
Now I know that the cluster identification occurs using bases 1-5 so I have thought about using a NNNNN after the sequencing primer. This should ensure that clusters are identified correctly.
However, for bases 6..15 all clusters have the same base. This will produce a single colour per flow, and there will potentially be optical effects due to saturation. Now, I don't really care about these bases, I am only interested in the genomic bases after the adaptor. So my question is: will the later bases be sequenced OK given that the early bases may have these problems?
Also, what will happen for the paired end read if that also has low complexity bases at the start? Since the cluster identification happens during the first read, the effect should be the same?
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