Help!! need a copy of config.xml file from GAIIx run

[liux]

Hi,

I need a copy of config.xml from a 100bp, single reads, GAIIx run (<runfolder>/Dana/Intensity/BaseCalls/config.xml)

a lab in the campus acquired a GAIIx machine. After the first run, they found the RTA was configured improperly (long story). Anyway, now all intensity, bcl, stat, filter, etc. files are intact, but config.xml file is missing. So we could not do BCL to qseq conversion.

But it could be re-constructed from a similar run. Well, it is the first run (other than a shorter phix test run earlier), they don't have a similar run. we modified a file from a 75bp reads run. But we run into errors later on.

So if you happen to have a run from GAIIx for 100 base reads, single end, with 108 cycles (I think it is indexed), we would appreciate a copy of <runfolder>/Dana/Intensity/BaseCalls/config.xml

thank you very much in advance!

X.L.

[GenoMax]

Have you contacted illumina tech support ([email protected]) with this request? They are very helpful.

[liux]

We did. And they told us how to modify the config.xml file. And that is how we modified the config.xml from a 75bp run.

after posting this yesterday, I further examined the config.xml from that 75bp run. In the end I updated the RTA version number in the file, then added _pos.txt file location parameter in the setupBclToQseq.py command, and I was able to run the conversion.

So problem might be solved. But I need to check the output files and make sure they are good.