General control lane used by Illumina/Solexa data?!

[edge]

I just read few article about the control lane used by Illumina/Solexa data.
After the process, it will got 8 lane at the end. Some said that normally Illumina/Solexa will use lane 4 as the control lane. But some said lane 5 and lane 8 as the control lane.
Anyone knows that which lane will be used by Illumina/Solexa as a control lane for sequencing process?
As I know that, remove the control lane before analyze the data is very important in data analyzing.
Thanks a lot for sharing info

[ScottC]

Hi,

The control sample can be in any lane. It is up to the operator to decide. Commonly, people will use lane 4 or 5 because they're in the middle of the flowcell and they suffer fewer artifacts. Sometimes, there is no control lane (again, it is up to the operator to either include or exclude a control).

Regards,

Scott.

[Patrick]

Hi ScottC,

Thanks for your suggestion. I appreciate it
For your opinion, normally what control lane will use for human genome process sequencing by Illumina/Solexa?
Thanks again

Hi,

The control sample can be in any lane. It is up to the operator to decide. Commonly, people will use lane 4 or 5 because they're in the middle of the flowcell and they suffer fewer artifacts. Sometimes, there is no control lane (again, it is up to the operator to either include or exclude a control).

Regards,

Scott.

[ScottC]

Hi,

Again, it could be any lane. There's no requirement for any particular lane. I usually run in lane 4 or 5, but not all the time.

If it's a human sample, there may not be any lane.

Your sequencing service provider will be able to tell you which lane contains the control. If not, you can probably do a quick alignment of the lanes to the PhiX174 phage genome - that's the Illumina-supplied control DNA.

Scott.

[Patrick]

Hi ScottC,

Really thanks a lot for your suggestion.
I understand what I should do now.
Thanks a lot ya
Hope that we can share our knowledge in future ^^

Hi,

Again, it could be any lane. There's no requirement for any particular lane. I usually run in lane 4 or 5, but not all the time.

If it's a human sample, there may not be any lane.

Your sequencing service provider will be able to tell you which lane contains the control. If not, you can probably do a quick alignment of the lanes to the PhiX174 phage genome - that's the Illumina-supplied control DNA.

Scott.

[simonandrews]

Just to point out that the default configuration for Illumina sequencers using pipeline 1.4 is that there is no control lane. The real time base calling uses data from all lanes to work out phasing information (which is one of the main purposes of the control).

If you want to use an explicit control lane you now need to reprocess your data on the pipeline server.

[james hadfield]

the next SCS software release will allow a control lane. Also the autofocus uses lane 4 (I think) so having the control there means theer should always be clutsers and that sequences should not be biased by adapter or library issues.