Forum:When to ask for rerun from vendors
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4.8 years ago
microfuge ★ 1.9k

Dear All,

I was wondering about the thumb rules used to flag a concern to sequencing data vendors. Previously we had sample swaps where the library types were swapped and they did the rerun for free. But when to draw a line for per base quality or tile failure. Some thumb rule like if x percent of bases below a y phred score then raise a flag. It would be good to know your experience and advice.

Thanks!

ngs-vendor • 942 views
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Several sequencing providers have minimum standards and will rerun if output falls bellow these standards - it is good practice to ask before contracting the service. Also, if output quality falls too much bellow the vendor specifications, e.g. 80% or less than the vendor specification, there is a good case for complain.

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4.7 years ago
GenoMax 143k

If your sequencing vendor has a document that describes minimum deliverables (it is likely few publish this information on web, I was just looking on website of a rather large vendor who had all sort of information EXCEPT this on their site) then a good place to start would be to compare your results to that document. Many vendors will only guarantee the yield/quality, IF they make the libraries for your samples. No vendor is likely going to (or should) trust user made libraries (unless you have a long history of submissions with them) and apply the same deliverables guarantee.

That said a significant responsibility lies with vendors too. Sequencing companies will replace reagents/kits if they are shown to have defects (and vendor has a maintenance agreement on sequencer). In such cases it is sequencing vendor's responsibility to not release defective data. Even though there may be deadlines that could be looming for you as a customer you would want to get data that is of best possible quality. Things (outside vendor control, human errors) happen and as long as both parties are willing to work things out, end results should always be satisfactory.

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Two crucial points indeed:

Many vendors will only guarantee the yield/quality, IF they make the libraries for your samples.

and

Sequencing companies will replace reagents/kits if they are shown to have defects (and vendor has a maintenance agreement on sequencer).

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