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start [2015/05/13 20:42] ceisenhart [Team pages and results] Added a link to team 3 page for completeness |
start [2015/06/08 17:33] ceisenhart [Team pages and results] |
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| * [[computer_resources:campusrocks|Complete guide to campusRocks and SGE]] | * [[computer_resources:campusrocks|Complete guide to campusRocks and SGE]] | ||
| * [[Budget]] | * [[Budget]] | ||
| - | * [[RNA]] | + | * [[Specific task]] |
| - | * [[Specific Task]] | + | * [[Banana slug genome browser]] A guide for accessing and setting up the banana slug hub. |
| ===== Important pages of this wiki ===== | ===== Important pages of this wiki ===== | ||
| * [[Computer resources]] describes the computers and file systems available for this class, how to get an account, how the directories are organized, how to get file permissions set correctly, and so forth. | * [[Computer resources]] describes the computers and file systems available for this class, how to get an account, how the directories are organized, how to get file permissions set correctly, and so forth. | ||
| - | * [[Banana Slug Genome Browser]] will have a UCSC genome browser, once we get to the point of having few enough contigs that building a browser makes sense. | ||
| * [[Style guide]] will have suggestions for organizing content on the wiki. | * [[Style guide]] will have suggestions for organizing content on the wiki. | ||
| * [[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. | ||
| + | * [[Euchromatin and Heterochromatin]] | ||
| ====Team pages and results ==== | ====Team pages and results ==== | ||
| - | Each team is attempting to assemble the banana slug genome with a different assembly program. The results are posted in the team pages below. | + | The mitochondrion for the banana slug was assembled! |
| - | [[team_1_page| Meraculous: Team 1 page]] | + | [[mitochondrion_2015 | 2015 Mitochondrion assembly ]] |
| - | [[soapdenovo2|SOAPdenovo2: Team 2 page]] | + | Each team is attempting to assemble the banana slug genome with a different assembly program. The results are posted in the team pages below. The assemblies are in the /campusdata/BME235/S15_assemblies/ folder on the campusrocks server. |
| - | + | | Team page | Contig N50 | Scaffold N50 | Total bases | Path | | |
| - | [[0.10.13|SGA: Team 3 page]] | + | |[[team_1_page| Meraculous: Team 1 page]]| N/A | N/A | N/A | N/A | |
| - | + | |[[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| | |
| - | [[team_4_page| ABySS: Team 4 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_5_page| Discovar de novo: Team 5 page]] | + | |[[team_5_page| Discovar de novo: Team 5 page]]| 10,427 | 12,549 | Un | DiscovarDeNovo/firstFullRun/discovarDeNovoAssembly.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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