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start [2015/05/27 06:02] nsaremi soap run 3 |
start [2015/06/24 04:14] charles |
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| * [[Spring 2015 syllabus]] The lecture schedule and registered note takers. | * [[Spring 2015 syllabus]] The lecture schedule and registered note takers. | ||
| * [[Data overview]] Raw data and associated analysis. | * [[Data overview]] Raw data and associated analysis. | ||
| - | * [[Teams]] Each team is attempting an assembly with a different program. | + | * [[Teams]] Each team is attempting an assembly with a different program. |
| + | * [[Summer 2015]] A page to organize summer work. | ||
| * [[Style Guide|Complete guide for modifying the wiki]] | * [[Style Guide|Complete guide for modifying the wiki]] | ||
| * [[computer_resources:campusrocks|Complete guide to campusRocks and SGE]] | * [[computer_resources:campusrocks|Complete guide to campusRocks and SGE]] | ||
| * [[Budget]] | * [[Budget]] | ||
| * [[Specific task]] | * [[Specific task]] | ||
| - | * [[Banana slug genome browser]] A guide for accessing and setting up the banana slug hub. | + | * [[Banana slug genome browser]] A guide for accessing and setting up the banana slug hub. |
| + | * [[Backup directory]] Paths on Charles' hive account where assembly and raw data files are backed-up. | ||
| ===== Important pages of this wiki ===== | ===== Important pages of this wiki ===== | ||
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| * [[Lecture notes]] will have pointers to notes taken by the students for each lecture. Two students will be designated each lecture to take notes, but others are encouraged to add their own notes to the wiki pages. | * [[Lecture notes]] will have pointers to notes taken by the students for each lecture. Two students will be designated each lecture to take notes, but others are encouraged to add their own notes to the wiki pages. | ||
| * [[Other mollusk genomes]] has a list of other mollusks that have been sequenced, and where the data for them is. Prior mollusk genomes may be very useful in annotating the banana slug. | * [[Other mollusk genomes]] has a list of other mollusks that have been sequenced, and where the data for them is. Prior mollusk genomes may be very useful in annotating the banana slug. | ||
| - | * [[RNA]] | ||
| * [[Euchromatin and Heterochromatin]] | * [[Euchromatin and Heterochromatin]] | ||
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| | Team page | Contig N50 | Scaffold N50 | Total bases | Path | | | Team page | Contig N50 | Scaffold N50 | Total bases | Path | | ||
| |[[team_1_page| Meraculous: Team 1 page]]| N/A | N/A | N/A | N/A | | |[[team_1_page| Meraculous: Team 1 page]]| N/A | N/A | N/A | N/A | | ||
| - | |[[soapdenovo2|SOAP: Team 2 page]]| 1,388 | 12,629 | 2,140,710,711 | SOAPdenovo2/assemblyTask/SOAPdenovo2_run3_all/soapdenovo2_allAssembly_1.scafSeq| | + | |[[soapdenovo2|SOAP: Team 2 page]]| 8,033 | 11,000 | 2,293,889,058 (non gap approx) | SOAPdenovo2/assemblyTask/SOAPdenovo2_run3_all/soapdenovo2_allAssembly_1.scafSeq.gapclosed| |
| - | |[[0.10.13|SGA: Team 3 page]]| | | + | |[[0.10.13|SGA: Team 3 page]]| N/A | N/A | N/A | N/A | |
| |[[team_4_page| ABySS: Team 4 page]]| 2,669 | 3,063 | 2,446,362,204| | |[[team_4_page| ABySS: Team 4 page]]| 2,669 | 3,063 | 2,446,362,204| | ||
| - | |[[team_5_page| Discovar de novo: Team 5 page]]| **9,513** | **10,634** | 2,245,788,654 | DiscovarDeNovo/firstFullRun/discovarDeNovoAssembly.fasta | | + | |[[team_5_page| Discovar de novo: Team 5 page]]| 10,427 | 12,549 | 2,395,797,282 | DiscovarDeNovo/KolossusAssembly/discovarDeNovoKolossusAssembly.fasta | |
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| ===== Old pages of this wiki ===== | ===== Old pages of this wiki ===== | ||
| - | These links are several years old. Due to the speed in which bioinformatics moves, most if not all of this information will be outdated. | + | These links are several years old. Due to the speed in which bioinformatics moves, most if not all of this information will be outdated. |
| + | * [[RNA]] | ||
| * [[computer_resources:data|Data available]] lists the datasets that we have to assemble and annotate the genome. The data will not appear on the wiki itself (due to the size of the files), but descriptions of it and pointers to the files will. | * [[computer_resources:data|Data available]] lists the datasets that we have to assemble and annotate the genome. The data will not appear on the wiki itself (due to the size of the files), but descriptions of it and pointers to the files will. | ||
| * [[computer_resources:assemblies|Assemblies]] lists the attempted assemblies (separated into subdirectories by organism). | * [[computer_resources:assemblies|Assemblies]] lists the attempted assemblies (separated into subdirectories by organism). | ||
start.txt · Last modified: 2015/10/07 03:14 by karplus
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