Using some of the 12 multiplex tags

[bioinfosm]

We would like to use 6-8 of the 12 tags per lane available for Solexa sequencing. Has someone looked at 'what 6 of the 12 tags would be least interfering?' in order to get the most efficient results?

In other words, for a lane sequenced using 6 tags, there are reads that map to the other 6 tags as well (I allow 1 mis-match). So does using a particular set of those 6 tags make this cross-match less likely?

Cheers,
sm

[Torst]

Has someone looked at 'what 6 of the 12 tags would be least interfering?' in order to get the most efficient results?

Surely the Illumina software which writes the 'recipes' for the run will automatically choose the best subset when multiplexing?

I would guess it already has preconfigured recipes for all multiplexing sizes from 2 to 12.

[nilshomer]

We would like to use 6-8 of the 12 tags per lane available for Solexa sequencing. Has someone looked at 'what 6 of the 12 tags would be least interfering?' in order to get the most efficient results?

In other words, for a lane sequenced using 6 tags, there are reads that map to the other 6 tags as well (I allow 1 mis-match). So does using a particular set of those 6 tags make this cross-match less likely?

Cheers,
sm

You could design your own tags, and even incorporate error correction codes into the tags. We have done this successfully in our own lab, though with the low error rates of Illumina, the error correction is a bit overkill.