Relationship of coordinate to well position

[qkdlspf]

I'm interested in relating the coordinate position of the sequence to the real world position of the bead. Anyone know how this could be done?

Also do wells have a specific standard spacing. For instance are wells a certain number of pixels apart on the x or y axis center to center?

[nilshomer]

What sequencing technology?

[westerman]

Since 'qkdlspf' posted in the 454 area, I suspect qkdlspf is talking about the 454. :-)

As far as I know, and I don't know very much, the wells on the 454 are in fixed positions. Definitely different than SOLiD where the beads could be anywhere. I do not know of a way to cross-reference sequence names with position although I suspect that it is buried in the name.

[qkdlspf]

Yes I am talking about 454.

I have a text file (Fasta) that includes sequences associated with a pixel (i.e. x=1431 y=3333). However what I need is the center of the well for each sequence. This information might look like x=1431.7 y=333.2. When I look at the files in the cwf folder the readable files .txt and .xml files contain scant information.

I'm guessing the .wel files might have this information but they appear to be in binary. Do you know of any 3rd party software that might be able to give center positions to the wells. If I know the center positions of all the wells its very easy for me to write a program to connect DNA pixel locations to the nearest well center. Is there any 3rd party software that can return well center information.

[kmcarr]

Yes I am talking about 454.

I have a text file (Fasta) that includes sequences associated with a pixel (i.e. x=1431 y=3333). However what I need is the center of the well for each sequence.

What is the distinction you are making between the reported xy coordinates (what your call a pixel) and the well location? Roche's documentation calls these are the well coordinates.

[qkdlspf]

Roche might be calling them well coordinates but they do not represent the center of each well, rather a pixel inside or in the near vicinity of the well. What I need is the center. Since Roche puts nice rings around all the wells the information is somewhere, I'm guessing locked away in the binary of a .wel file.