What Are Ranges Of Solexa X And Y

Question

[W Langdon]

A fastq file for Solexa 3623 output contains header lines like: @SRR001783.1 BI080419HWI-EAS3220002FC208CCAAXX:7:1:159:839 length=36 I think 159:839 are the X:Y positions of the cluster. There seems to be some thought that quality might degrade if either the cluster is near the edge of the tile, or the clusters are too close together.

Does anyone know of the legitimate range for X or Y? I started assuming it was 0:1023 for both X and Y but that is wrong. Are the ranges the same for X and Y? Do they depend on the tile? Are they fixed?

Many thanks Bill

Answer 1

[biobot 0.0.77.a.1099]

It is the same for each tile. The dimension varies, depending on the chip version. In my old code for making heatmap images of the chips I have these comments:

• GA1 chips are 0-1004 on the x-axis, 0-1002 on the y-axis
• GA2 chips are 0-2048 square, but masked on the x-axis to 0-1794

I'm afraid I can't recall where I found this information. I don't know what the expected values are for a HiSeq.

[W Langdon]

Thanks Keith. Is the chip type saved in the fastq file? Or encoded elsewhere? Bill

[biobot 0.0.77.a.1099]

No, it's not. You'll need to ask your data provider for the platform details.