We have been running many libraries with a core using the PE 300 kit on their MiSeqs. We've been working with them successfully for more than a year, and I've been using a set protocol for at least a couple successful runs.
Two months ago, they ran three of our libraries and read 2 (read 3, technically, we have indices) was completely unusable. Quality was well below 20 within just a few cycles. Read 1 was otherwise normal. Unfortunately for our project, our required reads are >300bp so we require both reads. I was immediately concerned that something was wrong with the adapters or index mixes, but they informed us that they saw the same problem among multiple samples. They said that it was a problem with Illumina's reagents. I have no reason to doubt them, but I didn't see anything here on a cursory search and they still haven't sequenced anything.
Does anyone know about this? What happened and when is it expected to be fixed? We're in a huge time crunch as our money source is about to cut us off and I have a ton of libraries that need sequencing. Any information and help would be appreciated.
Two months ago, they ran three of our libraries and read 2 (read 3, technically, we have indices) was completely unusable. Quality was well below 20 within just a few cycles. Read 1 was otherwise normal. Unfortunately for our project, our required reads are >300bp so we require both reads. I was immediately concerned that something was wrong with the adapters or index mixes, but they informed us that they saw the same problem among multiple samples. They said that it was a problem with Illumina's reagents. I have no reason to doubt them, but I didn't see anything here on a cursory search and they still haven't sequenced anything.
Does anyone know about this? What happened and when is it expected to be fixed? We're in a huge time crunch as our money source is about to cut us off and I have a ton of libraries that need sequencing. Any information and help would be appreciated.
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