on outsourcing and data management - icrisat
on outsourcing and data management - icrisat on outsourcing and data management - icrisat
Outsourcing • Lets suppose we have done the groundwork. We know what we want to do and why. • So where do we go ? Its not rocket science ! • The first step is to talk through our requirements with several potential providers and or try and identify and talk to some groups who have already done the sort of thing you have in mind, • Be aware that we are ALL amateurs in this game with few exceptions. So don’t trust the hype from commercial or academic providers. • Look for experience in preparing the library types you want to sequence and ideally plant tissue sources. • Who picks up the tab if a library construction of sequence run fails ?
Once you have made the choice • Make sure you know what you are getting and when. We have had several experiences of people generating our data in little bits and squirting it back to us in sporadic lumps. • A professional provider will know and understand their service and should give you good stats / metadata on a run. Ask them to provide you with some examples of this • Sequence a little first and then check what you have. Eg. Start with a lane and then check for things like redundancy length distribution, chloroplast contamination etc depending on your project. • This QC checking needs to start early in the process. It’s no use finding its all crap when all the money is spent. • It took us months to begin to learn what the issues are. We are still learning
- Page 1 and 2: Outsourcing and Data handling Issue
- Page 3 and 4: Outsourcing • We don’t own a ma
- Page 5: What are we sequencing and why ?
- Page 9 and 10: Processing and analysis • We disc
- Page 11: NGS Meetings
Once you have made the choice<br />
• Make sure you know what you are getting <strong>and</strong> when. We have<br />
had several experiences of people generating our <strong>data</strong> in little<br />
bits <strong>and</strong> squirting it back to us in sporadic lumps.<br />
• A professi<strong>on</strong>al provider will know <strong>and</strong> underst<strong>and</strong> their<br />
service <strong>and</strong> should give you good stats / meta<strong>data</strong> <strong>on</strong> a run.<br />
Ask them to provide you with some examples of this<br />
• Sequence a little first <strong>and</strong> then check what you have. Eg. Start<br />
with a lane <strong>and</strong> then check for things like redundancy length<br />
distributi<strong>on</strong>, chloroplast c<strong>on</strong>taminati<strong>on</strong> etc depending <strong>on</strong> your<br />
project.<br />
• This QC checking needs to start early in the process. It’s no<br />
use finding its all crap when all the m<strong>on</strong>ey is spent.<br />
• It took us m<strong>on</strong>ths to begin to learn what the issues are. We are<br />
still learning
Change language