Courageous Cantaloupe: Difference between revisions
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March 2010, third public data release through [https://proteomecommons.org/tranche/ ProteomeCommons.org's Tranche Network]<br/> | |||
====Collaborators==== | ====Collaborators==== | ||
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===Content=== | ===Content=== | ||
* Raw images | * Raw images from targeted capture experiments from PGP1-5,PGP7-10. | ||
* PGP reads from GA Pipeline 1.0 | * PGP reads from GA Pipeline 1.0, 1.3.2, Swift. | ||
* Alignment results and raw reads from all [http://snp.med.harvard.edu Trait-o-matic genomes] | |||
* | * Data from accepted [[PGP:Publications|Publications]]: | ||
* | ** Add [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp383 Bioinformatics]... | ||
* | ** Add [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08211.html Nature]... | ||
* [http:// | ** Add [http://www.sciencemag.org/cgi/content/abstract/1181498 Science]... | ||
* | ** Add ... | ||
** [ | * Free and open source software in use at PGP: | ||
** [http:// | ** [https://trac.scalablecomputingexperts.com/wiki/Trait-o-matic Trait-o-matic] | ||
** [https://trac.scalablecomputingexperts.com/wiki Free Factories] | |||
* Other free and open-source software of interest: | |||
** [http://boinc.berkeley.edu/ BOINC] & [http://boinc.berkeley.edu/trac/wiki/BossaIntro BOSSA] | |||
** [http://www.ubuntu.com/cloud Ubuntu Cloud] | |||
** [http://www.eucalyptus.com/ Eucalyptus] | ** [http://www.eucalyptus.com/ Eucalyptus] | ||
===PeoplePower and StatusUpdate=== | ===PeoplePower and StatusUpdate=== | ||
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* Software | * Software | ||
* [http://boinc.berkeley.edu/ BOINC] application | * [http://boinc.berkeley.edu/ BOINC] application | ||
** | ** David Anderson suggested we start by using the mailing lists. | ||
** He is mostly focused on [http://boinc.berkeley.edu/trac/wiki/BossaIntro Bossa] and I can't help wonder if we should be focused on Bossa ourselves. It would be very impressive to have our community of volunteers helping to populate a database of genetic variants by culling the literature and performing other tasks. See http://stardustathome.ssl.berkeley.edu/ for an example of the sort of project that Bossa is intended to facilitate. Also see Amazon's [https://www.mturk.com/mturk/welcome Mechanical Turk] | |||
'''BKG:'''<br/> | '''BKG:'''<br/> | ||
* [http://boinc.berkeley.edu/ BOINC] application | * [http://boinc.berkeley.edu/ BOINC] application | ||
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* fold Tranche up-/download tools into [http://boinc.berkeley.edu/ BOINC] application | * fold Tranche up-/download tools into [http://boinc.berkeley.edu/ BOINC] application | ||
<br/> | <br/> | ||
===Data Processing=== | |||
'''AL:''' I have processed the following data with GAP1.3.2 and Swift: <br/> | |||
'''Processed:'''<br/> | |||
PGP1: PGP1_37_003 <br/> | |||
PGP2: PGP2_37_002 <br/> | |||
PGP3: PGP3_35_003 <br/> | |||
PGP4: PGP4_43_002 <br/> | |||
PGP5: PGP5_44_002 <br/> | |||
PGP8: PGP8_51_002, PGP8_37_001 <br/> | |||
PGP9: PGP9_43_003 <br/> | |||
PGP10: PGP10_41_003 <br/> | |||
'''Open:''' <br/> | |||
PGP7_44_004<br/> | |||
PGP8_51_006<br/> | |||
PGP9_51_003, PGP9_51_007 <br/> | |||
'''Notes: '''<br/> | |||
PGP5_44_002 stacks 95-100 could not be processed with Swift. Nava implemented a bug fix to Swift, needs rerun with latest Swift version. <br/> | |||
PGP9_43_003 stacks 1,2 .fastq and .nonpf missing, need rerun <br/> | |||
PPG6: Do not process, redacted.<br/> | |||
'''Data location:'''<br/> | |||
Complete Swift results including raw intensity files and reads are at /boinc-dev-scractch/PGP* <br/> | |||
Complete RunFolders from GAP1.3.2 are at /boinc-scratch/RunFolder* |
Latest revision as of 13:15, 30 November 2009
March 2010, third public data release through ProteomeCommons.org's Tranche Network Collaborators
Content
PeoplePower and StatusUpdateAL:
BKG:
Data ProcessingAL: I have processed the following data with GAP1.3.2 and Swift:
|