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Old 05-10-2011, 10:08 AM   #1
HMorrison
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Default need test dataset for OLB

How can I get a test dataset for OLB 1.9? I realize they are huge, but we need one (with config.xml, filter/bcl/txt files...the works). Can NOT get setupBclToQseq.py to run.
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Old 05-10-2011, 11:10 PM   #2
simonandrews
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Can't help with the dataset, but we also had a problem with setupBclToQseq. In our case the problem appeared to be that we tried to run GERALD before having done the qseq conversion. This obviously failed, but also seemed to change something which then made setupBclToQseq fail (it just sat in an infinite loop writing out the same config files over and over again).

We spent a while troubleshooting this with Illumina tech support but in the end we gave up and reprocessed from intensities.

If your problem is similar and you get to the bottom of it I'd be interested to hear what it was.
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Old 05-12-2011, 05:02 AM   #3
HMorrison
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Quote:
Originally Posted by simonandrews View Post
Can't help with the dataset, but we also had a problem with setupBclToQseq. In our case the problem appeared to be that we tried to run GERALD before having done the qseq conversion. This obviously failed, but also seemed to change something which then made setupBclToQseq fail (it just sat in an infinite loop writing out the same config files over and over again).

We spent a while troubleshooting this with Illumina tech support but in the end we gave up and reprocessed from intensities.

If your problem is similar and you get to the bottom of it I'd be interested to hear what it was.
The latest we've heard is that BclConverter that's included in OLB 1.9.0 is incompatible with HiSeq RTA version installed (last month!!)--I can't understand why the problem is unique to our site. No one here has been terrifically impressed by the troubleshooting abilities of Illumina folks, both at hardware and s/w end. Next step is to install v 1.9.1, apparently just made available at iCom site yesterday...then to try it all again.
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Old 01-27-2012, 11:54 AM   #4
MRSeq
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Hello,

did you solve the problem. I am also looking for a test data for OLB - can you point me to some or share yours? I know these are huge files but at least we are both on the same side of the pond :-)
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Old 01-27-2012, 12:24 PM   #5
HMorrison
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Default No dataset found

Never got one, sorry. We are using CASAVA 1.8 at this stage, so it's all one step.
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Old 01-27-2012, 12:30 PM   #6
MRSeq
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Hi Hillary,

Thank you for such a prompt answer. I would actually would like to use OLB for image analysis - if I understand correctly, the image analysis functionality is still there, using it is just deprecated. Therefore, CASAVA would not solve our problems. Anyway, it would be nice to have a complete HiSeq test data set available.
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