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Old 01-19-2016, 03:31 PM   #23
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Originally Posted by melop View Post
I see. But is that a common practice to let the end user bare the loss even if the facility prepares the library knowing that they are going on a HiSeq 4000? I understand that if Illumina agrees to replace the reagents then there will be no problem, but I will be surprised if that should become the end user's burden if such a performance issue is caused by inadequate library prep (say insert size not tight enough or negligence in adapter cleaning, suggested by previous posts). One problem is that this core does not have any written policy regarding quality, and their policies all seem to be post hoc .....
You are referring to two separate issues and they need to be addressed separately. Sounds like you are ok with the run metrics explanation.

If you have questions about the quality of the libraries that were prepared then ask the facility to share their library QC data with you. Ask them if they bead treated the libraries as recommended? If the libraries look suboptimal then they may need to clean them up and re-run your samples at no cost. Again things you should discuss in good faith with your facility.

There are current instances (e.g. MiSeq 2x300 kits) where dismal Q-scores seem to rule late in read 2 but that does not affect the actual sequence. That may apply in your case as well. You may have perfectly good sequence data that has a Q-score issue that people have been discussing in this thread.

Last edited by GenoMax; 01-19-2016 at 03:35 PM.
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