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Automatic or Geneus-driven merging of multiple lanes from same library #44

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
We often sequence multiple lanes from the same NGS library. Unless one of the 
lanes is a failure, these almost always have to be merged.  We originally had a 
plan for doing this manually via a Geneus mechanism (an "re-analysis" process, 
which also contained analysis parameters).  While the idea of a Geneus analysis 
process is appealing (it can contain modifiable analysis parameters), it also I 
think makes sense to simply merge lanes for the same library and regenerate QC 
reports automatically.

In order to implement, Geneus would have to be polled regularly, and multiple 
merges might have to be done for the same library (for instance if we have a 
lane of the library on 3 successive flow cells). It also needs UI support, as 
these will need to be added to the library-centric ECCP view.

Original issue reported on code.google.com by benb...@gmail.com on 11 Apr 2011 at 4:10

GoogleCodeExporter commented 8 years ago

Original comment by benb...@gmail.com on 11 Apr 2011 at 4:11

GoogleCodeExporter commented 8 years ago

Original comment by benb...@gmail.com on 11 Apr 2011 at 4:12

GoogleCodeExporter commented 8 years ago 
Since there us UI and geneus interface stuff, I want Tejas to assist, and lead 
devel on this if possible. I can handle the backend pipeline part

Original comment by zack...@gmail.com on 11 Apr 2011 at 11:21

GoogleCodeExporter commented 8 years ago 
We need to discuss this as a general topic though.  I'm not sure the Geneus 
implementation is realistic at this point.  It might be easier and more 
realistic just to have a daemon that does it all on the backend and 
automatically puts results into ECCP database. Samples from the same library 
are easily identifiable from the Geneus ID.

Original comment by benb...@gmail.com on 11 Apr 2011 at 11:26

GoogleCodeExporter commented 8 years ago 
we should have everything we need to match samples using our existing 
mysql://epifire2/sequencing db. It gets regenerated every night from geneus and 
contains sample meta as well integrating derived qc results.

Original comment by zack...@gmail.com on 11 Apr 2011 at 11:35

GoogleCodeExporter commented 8 years ago

Original comment by zack...@gmail.com on 6 Feb 2012 at 11:45

GoogleCodeExporter commented 8 years ago 
We increasingly need this for NOMe-seq and WGBS.  We need to be able to merge 
and automatically run pipeline up to and including Bis-SNP.

Original comment by benb...@gmail.com on 31 Jul 2012 at 7:20

GoogleCodeExporter commented 8 years ago

Original comment by benb...@gmail.com on 31 Jul 2012 at 7:20

GoogleCodeExporter commented 8 years ago

Original comment by zack...@gmail.com on 31 Jul 2012 at 7:59

GoogleCodeExporter commented 8 years ago 
this is still an ongoing issue and is not forgotten

Original comment by zack...@gmail.com on 8 Nov 2012 at 10:51

GoogleCodeExporter commented 8 years ago 
we have an automated pipeline for merging, we just need to kick it off with 
geneus

Original comment by zack...@gmail.com on 4 Dec 2012 at 10:20

GoogleCodeExporter commented 8 years ago 
this is pretty much done, added as part of the backend rewrite.

Original comment by zack...@gmail.com on 28 Feb 2013 at 11:32

GoogleCodeExporter commented 8 years ago 
closing this general issue. 

submit specific problems as a new ticket

Original comment by zack...@gmail.com on 14 Mar 2013 at 11:28

GoogleCodeExporter commented 8 years ago 
Issue 432 has been merged into this issue.

Original comment by zack...@gmail.com on 14 Mar 2013 at 11:29