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archive:specific_task [2015/05/26 17:03]
jdhouser
archive:specific_task [2015/08/04 03:32] (current)
68.180.228.52 ↷ Links adapted because of a move operation
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 |Task| Assignee | Status | Notes| |Task| Assignee | Status | Notes|
-|Find virus contigs and use PRICE to expand to full viruses | Cole,​jolespin | | jolespin virus assembly progress can be accessed at [[jolespin_virus]]|+|Install Maker| Houser | Complete | Maker is installed, see information [[archive:​maker|here]] | 
 +|Assemble repeat genome with RepArk|Team 1|In progress|Charles has started a test run using the original Hiseq and Miseq reads| 
 +|Run GapCloser on SOAP denovo assembly|Charles|In progress| Use SOAP denovo'​s external gap closer. Chose a reasonable name for new assembly. | 
 +|Find virus contigs and use PRICE to expand to full viruses | Cole,​jolespin | | jolespin virus assembly progress can be accessed at [[archive:jolespin_virus]]|
 | Mate-pair adapter and linker removal| ​ | | | | Mate-pair adapter and linker removal| ​ | | |
 | Measuring insert size for each mate-pair library | unassigned | | | | Measuring insert size for each mate-pair library | unassigned | | |
 | Making Seqprep, adapter removed, end-trimmed library files | unassigned | | | | Making Seqprep, adapter removed, end-trimmed library files | unassigned | | |
-| Blast long contigs and analyze results | Houser| | Check the browser for the 30 longest contigs from each group with contigs| ​+| Blast long contigs and analyze results | unassigned| | Check the browser for the 30 longest contigs from each group with contigs| ​
 | Find genes in the mitochondrial genome | unassigned | | The genome is on the browser, find it here https://​banana-slug.soe.ucsc.edu/​banana_slug_genome_browser |  | Find genes in the mitochondrial genome | unassigned | | The genome is on the browser, find it here https://​banana-slug.soe.ucsc.edu/​banana_slug_genome_browser | 
 | Use PRICE to get mitochondrial genome as single contig | Natasha Dudek? | | | | Use PRICE to get mitochondrial genome as single contig | Natasha Dudek? | | |
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 | End trim SeqPrepped data | Hussain | | |  | End trim SeqPrepped data | Hussain | | | 
 | Error correct SeqPrepped data | McGovern | waiting on previous step | |  | Error correct SeqPrepped data | McGovern | waiting on previous step | | 
 +| Error Correction new data| McGovern (Musket) | In progress |  |
 +| Install bowtie | Chaves | In progress |/​campusdata/​gchaves/​Bowtie/​bowtie2-2.2.5 (Not yet running successfully)|
 | UCSC Genome browser hub | Eisenhart | Complete | https://​banana-slug.soe.ucsc.edu/​banana_slug_genome_browser |  | UCSC Genome browser hub | Eisenhart | Complete | https://​banana-slug.soe.ucsc.edu/​banana_slug_genome_browser | 
 | Plot contig size histogram for current assembly (SOAPdenovo2 results) | Markello | Complete | | | Plot contig size histogram for current assembly (SOAPdenovo2 results) | Markello | Complete | |
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 | Find cost of creating a tagmentase library| Dudek | | ~$50 | | Find cost of creating a tagmentase library| Dudek | | ~$50 |
 | Merge/trim new data (SeqPrep) | Hussain | Completed | See wiki page for each data set for details | | Merge/trim new data (SeqPrep) | Hussain | Completed | See wiki page for each data set for details |
-| Analyze new data (preqc) | Richardson | In progress ​{{:​ucsf_new_lib_preqc_report.pdf|}}| ​  +| Analyze new data (preqc) | Richardson | Completed ​See wiki page for each data set for details ​
-| Error Correction new data| McGovern (Musket) & Richardson (BLESS/​racer) | In progress | These programs have not yet been run succesfully... | +
-| Install bowtie | Chaves | In progress |/​campusdata/​gchaves/​Bowtie/​bowtie2-2.2.5 (Not yet running successfully)|+
 | Preqc on new mate pair SW041 SW042| Saremi | Completed | | | Preqc on new mate pair SW041 SW042| Saremi | Completed | |
 | Update the wiki to include mate pair meta data | Eisenhart | completed |  | Update the wiki to include mate pair meta data | Eisenhart | completed | 
archive/specific_task.1432659816.txt.gz · Last modified: 2015/05/26 17:03 by jdhouser