We're sequencing a mammalian genome on RSII for ~70x coverage so we're seeking to sequence approx 300 (or more) SMRT cells.
We've done 80 SMRT cells so far and we're trying to recalculate the number of SMRT cells we need to sequence.
Looking at the finished SMRT cells, we found that P1 values correlate with yield quite well when ranging between 25~45%, but read length (average length and N50) don't seem to be affected by P1 value. P1 of 45% would give ~750Mb per cell, while P1 of 37% would give a bit less than 600Mb per cell.
We were told 37% would be the optimal value for P1 to get the best read quality, but from a cost saving perspective, having a hight P1 value (e.g. 45%) would lead to a higher output and save quite a big number of SMRT cells needed.
Does anyone have any experience on getting an optimal P1 value to achieve both high quality of reads and higher yield per SMRT cell? Any comments will be appreciated.
We've done 80 SMRT cells so far and we're trying to recalculate the number of SMRT cells we need to sequence.
Looking at the finished SMRT cells, we found that P1 values correlate with yield quite well when ranging between 25~45%, but read length (average length and N50) don't seem to be affected by P1 value. P1 of 45% would give ~750Mb per cell, while P1 of 37% would give a bit less than 600Mb per cell.
We were told 37% would be the optimal value for P1 to get the best read quality, but from a cost saving perspective, having a hight P1 value (e.g. 45%) would lead to a higher output and save quite a big number of SMRT cells needed.
Does anyone have any experience on getting an optimal P1 value to achieve both high quality of reads and higher yield per SMRT cell? Any comments will be appreciated.
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