contributors:team_5_page
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contributors:team_5_page [2015/05/16 03:00] ceisenhart [Fasta assemblies] |
contributors:team_5_page [2015/07/18 20:30] ceisenhart ↷ Page moved from team_5_page to contributors:team_5_page |
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| The raw data was received as fastq pairs. Each pair contains a forward and reverse strand. These pairs are ran through Skewer to remove adaptor sequences, then ran through fastUniq to remove PCR duplicates. Next the forward and reverse strand are merged into a single unaligned BAM file. | The raw data was received as fastq pairs. Each pair contains a forward and reverse strand. These pairs are ran through Skewer to remove adaptor sequences, then ran through fastUniq to remove PCR duplicates. Next the forward and reverse strand are merged into a single unaligned BAM file. | ||
| - | {{:flowchart5.4.2015.png}} | + | {{:fastqtobam.png}} |
| All unaligned BAM files are then passed into Discovar //de novo//. The output is an assembly in .fasta format and Discovar //de novo// visualization files. The .fasta file can then be re-scaffolded with a scaffolding program (see next workflow). The finished file can be represented on the UCSC genome browser. | All unaligned BAM files are then passed into Discovar //de novo//. The output is an assembly in .fasta format and Discovar //de novo// visualization files. The .fasta file can then be re-scaffolded with a scaffolding program (see next workflow). The finished file can be represented on the UCSC genome browser. | ||
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| |[[team_5_page:50PerRun | 50% data]]| (Post Skewer and FastUniq) MiSeq data SW019_S1_L001, HiSeq data SW018_S1_L007, HiSeq data SW019_S2_L008 | | |[[team_5_page:50PerRun | 50% data]]| (Post Skewer and FastUniq) MiSeq data SW019_S1_L001, HiSeq data SW018_S1_L007, HiSeq data SW019_S2_L008 | | ||
| |[[team_5_page:50PerRunUCSF | 50% data UCSF]]| (Post Skewer and FastUniq) UCSF SW018 and SW019 data | | |[[team_5_page:50PerRunUCSF | 50% data UCSF]]| (Post Skewer and FastUniq) UCSF SW018 and SW019 data | | ||
| + | |[[team_5_page:FullRun1 | Full data run 1]] | (Post Skewer and FastUniq) 100% of the MiSeq SW019, UCSF SW019, and 50 % BS-tag datasets | | ||
| + | |[[team_5_page:KollosusFullRun | Kolossus full run]] | (Post Skewer and FastUniq) 100% of the MiSeq SW019, UCSF SW019, UCSF SW018, BS-tag, BS-MK datasets | | ||
| The logs are very large, important statistics have been gathered and are compared below. | The logs are very large, important statistics have been gathered and are compared below. | ||
| Note that MPL1 is an acronym for mean length of first read in pair up to first error. | Note that MPL1 is an acronym for mean length of first read in pair up to first error. | ||
| - | | | 1% run | 5% run | 10 % run| 50 % run | 50% UCSF run | | + | | | 1% run | 5% run | 10 % run| 50 % run | 50% UCSF run | FullRun1 | Kollosus full run | |
| - | | Total runtime | 1.75 hours| 1.53 hours| 2.4 hours| 8.53 hours| 14.9 hours | | + | | Total runtime | 1.75 hours| 1.53 hours| 2.4 hours| 8.53 hours| 14.9 hours | 24.2 hours| 103 hours | |
| - | | Peak memory use | 43.92 GB | 78.10 GB| 151.05 GB| 220.11 GB | 184.09 GB| | + | | Peak memory use | 43.92 GB | 78.10 GB| 151.05 GB| 220.11 GB | 184.09 GB| 246.03 GB| 583.25 GB | |
| - | | Bases in 1kb+ scaffolds| 75,233 | 592,685 | 1,476,875 | 101,397,871 | 1,528,625,509 | | + | | Bases in 1kb+ scaffolds| 75,233 | 592,685 | 1,476,875 | 101,397,871 | 1,528,625,509 | 1,849,167,875 | 1,885,373,341| |
| - | | Bases in 10kb+ scaffolds| 10,572 | 11,088 | 168,543 | 151,417 | 137,959,107 | | + | | Bases in 10kb+ scaffolds| 10,572 | 11,088 | 168,543 | 151,417 | 137,959,107 | 972,798,485 | 1,106,140,476 | |
| - | | MPL1 | 2 | 2 | 3 | 7 | 156 | | + | | MPL1 | 2 | 2 | 3 | 7 | 156 | 169 | 169 | |
| - | | Contig N50 | 2,622 | 2,067 | 2,563 | 1,489 | 3,979 | | + | | Contig N50 | 2,622 | 2,067 | 2,563 | 1,489 | 3,979 | 9,513 | 10,427 | |
| - | | Scaffold N50 | 2,622 | 2,067 | 2,563 | 1,489 | 3,979 | | + | | Scaffold N50 | 2,622 | 2,067 | 2,563 | 1,489 | 3,979 | 10,634 | 12,549 | |
| + | | Coverage | | | | | 16x | 47x | 80X | | ||
| ====Fasta assemblies==== | ====Fasta assemblies==== | ||
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| /campusdata/BME235/S15_assemblies/DiscovarDeNovo | /campusdata/BME235/S15_assemblies/DiscovarDeNovo | ||
| - | Each fasta assembly is in its own directory, the directory name is the assembly name. Currently there are five assemblies, The final fasta file is name a.lines.fasta. Note there was an issue using the a.fasta file which contains the reverse complement of every contig. Consequently statistics were falsely reported as twice the actual number until May 15th 2015 when the error was noted. The statistics have since been corrected. | + | Each fasta assembly is in its own directory, the directory name is the assembly name. Currently there are five assemblies, The final fasta file is name a.lines.fasta. Note originally the authors used the a.fasta file (which contains the reverse complement of every contig) for statistics. Consequently statistics were falsely reported as twice the actual number until May 15th 2015 when the error was identified. The statistics have since been corrected. |
| Raw stats were mined from the fasta files using a python script fastaStats.py. The script is available online at (https://github.com/ChrisEisenhart/binfProgs/blob/master/basicProgs/fastaStats.py). | Raw stats were mined from the fasta files using a python script fastaStats.py. The script is available online at (https://github.com/ChrisEisenhart/binfProgs/blob/master/basicProgs/fastaStats.py). | ||
| - | **NOTE for all statistics listed below the scaffolds and contigs are identical** | ||
| |Assembly name| Bytes | Total bases | # scafs | Av. scaf len | Longest scaf | Scaf N50 | # Scaf > 5Kb | Bases in 10kb+ scafs| | |Assembly name| Bytes | Total bases | # scafs | Av. scaf len | Longest scaf | Scaf N50 | # Scaf > 5Kb | Bases in 10kb+ scafs| | ||
| |1%run| 463K | 448,486 | 2,558 | 350 | 5,385 | 2,622| | 10,572 | | |1%run| 463K | 448,486 | 2,558 | 350 | 5,385 | 2,622| | 10,572 | | ||
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| |10%run| 7.5 M | 7,382,612 | 38,195 | 386 | 11,911 | 2,563 | | 168,543 | | |10%run| 7.5 M | 7,382,612 | 38,195 | 386 | 11,911 | 2,563 | | 168,543 | | ||
| |50%run| 137 M | 137,695,736 | 273,653 | 1,006 | 19,658 | 1,489 | | 151,417 | | |50%run| 137 M | 137,695,736 | 273,653 | 1,006 | 19,658 | 1,489 | | 151,417 | | ||
| - | |UCSF50%run | 1.9 G | 1,839,371,352 | 3,094,953 | 1,261| 34,857 | 3,979 | 138,226 | 137,959,107 | | + | |UCSF50%run | 1.9 G | 1,839,371,352 | 1,126,557 | 1,632| 55,757 | 3,979 | 80,721 | 137,959,107 | |
| + | |firstFullRun | 2.2G | 2,245,788,654 | 1,450,447 | 1,548 | 153,999 | 10,634 | 118,545 | 972,798,485 | | ||
| + | |Kolossus full run | 2.4G | 2,395,797,282 | 1,843,153 | 1299 | 129,831 | 12,549 | 113,978 | 1,106,140,476 | | ||
| - | The latest run assembled 138,226 scaffolds longer than 5000 base pairs. This accounts for roughly 30% of the banana slug genome. The scaffolds longer than 5,000 base pairs were separated and put at the following location; | + | The absolute path to our latest assembly in .fasta format is; |
| - | + | ||
| - | /campusdata/BME235/S15_assemblies/DiscovarDeNovo/UCSF50%run/bigContigs.fa | + | |
| + | /campusdata/BME235/S15_assemblies/DiscovarDeNovo/KolossusAssembly/discovarDeNovoKolossusAssembly.fasta | ||
| Looking at the 10% run, the majority of scaffolds generated are quite short (<1kb). | Looking at the 10% run, the majority of scaffolds generated are quite short (<1kb). | ||
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| {{:histogram_for_ucsf_50_run.png?200|}} | {{:histogram_for_ucsf_50_run.png?200|}} | ||
| - | + | ||
| - | The banana slug genome is estimated to be 2.1 billion bases (2,800 million), our latest run has assembled just under 2 billion bases! | + | |
| ====Post assembly scaffolding==== | ====Post assembly scaffolding==== | ||
| The program SSPace (documentation below) was used to scaffold the the assembly with mate pair data. The UCSF SW041 and SW042 mate pair libraries were used to generate the library.txt file. | The program SSPace (documentation below) was used to scaffold the the assembly with mate pair data. The UCSF SW041 and SW042 mate pair libraries were used to generate the library.txt file. | ||
| - | [[team_5_page:SSPaceSummaryFile | SSpace summary file ]] | + | [[team_5_page:SSPaceSummaryFile | SSpace summary file UCSF 50% ]] |
| + | |||
| + | [[team_5_page:SSPaceSummaryFile2 | SSpace summary file firstFullRun ]] | ||
contributors/team_5_page.txt · Last modified: 2015/09/04 14:56 by 157.55.39.159
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