I just did my first sequencing run on the GAIIx. I was doing some quality control calculations from the data contained in the Summary File and I noticed something that I didnt' expect to see.
i had very clear peaks (maxima) in the cluster density around Tile 1 and Tile 120 with a minima in the middle. In other words, the graph of Tile # (X-axis) versus Cluster Density (Y-axis) looks like a parabola.
For lanes whose cluster density ranged from 150,000 to 220,000 the amount of mappable sequence was proportional (though not linearly) to the cluster density; while for the lanes that had between 230,000 and 250,000 clusters per tile, the trend seemed to be inversely proportional.
As expected, Lane 8 was yielded <50% mappable reads of the ones that passed filter with a large amount not passing filters but it clearly had this parabolic distribution across the lane's tiles.
My question is, does the parabolic cluster density reflect problems with the optics of detecting clusters, a problem with the flowcell, or a problem with the pump on the cluster generation station? or is this a normal pattern in your experience? Secondly, what order are the tiles on the flowcell? is it a 2x60 or a 1x120 or 3x40 design for each lane?
Thanks,
der.
PS. i should clarify that these numbers are before QC. the numbers after QC are not parabolic when graphed.
i had very clear peaks (maxima) in the cluster density around Tile 1 and Tile 120 with a minima in the middle. In other words, the graph of Tile # (X-axis) versus Cluster Density (Y-axis) looks like a parabola.
For lanes whose cluster density ranged from 150,000 to 220,000 the amount of mappable sequence was proportional (though not linearly) to the cluster density; while for the lanes that had between 230,000 and 250,000 clusters per tile, the trend seemed to be inversely proportional.
As expected, Lane 8 was yielded <50% mappable reads of the ones that passed filter with a large amount not passing filters but it clearly had this parabolic distribution across the lane's tiles.
My question is, does the parabolic cluster density reflect problems with the optics of detecting clusters, a problem with the flowcell, or a problem with the pump on the cluster generation station? or is this a normal pattern in your experience? Secondly, what order are the tiles on the flowcell? is it a 2x60 or a 1x120 or 3x40 design for each lane?
Thanks,
der.
PS. i should clarify that these numbers are before QC. the numbers after QC are not parabolic when graphed.
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