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archive:specific_task [2015/05/10 22:07]
ndudek
archive:specific_task [2015/05/27 01:11]
jennie
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 |Task| Assignee | Status | Notes| |Task| Assignee | Status | Notes|
-Map lucigen mates against scaffolds ​to estimate insert size Dudek Completed ​There seem to be technical issues with the lucigen mate pair reads. Average read length is 40bp and average ​insert size is ~220bpcompared to an expected read length of 300bp and insert size over 1kb. AlsoI spoke with Brendan ​and there is new mate-pair data coming soon (expected ​the week of May 10th). | +|Find virus contigs and use PRICE to expand to full viruses ​Cole,​jolespin ​| | jolespin virus assembly progress can be accessed at [[jolespin_virus]]| 
-| Plot contig size vs total genome size for assemblies | | | | +| Mate-pair adapter ​and linker removal| ​ | | | 
-| Plot contig size histogram for current assembly (SOAPdenovo2 results) | Markello | In progress ​| | +| Measuring ​insert size for each mate-pair library | unassigned | | | 
-| Plot scaffold size histogram for current assembly (SOAPdenovo2 results) | Markello | In progress | | +| Making Seqprepadapter removedend-trimmed library files | unassigned | | | 
-| Ask UCSF about the discrepancy in the numbers of reads | | | | +| Blast long contigs ​and analyze results | Houser| | 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 |  
 +| Use PRICE to get mitochondrial genome as single contig | Natasha Dudek? | | 
 +| Plot contig size vs total genome size for assemblies | unassigned ​| | 
 +| Ask UCSF about the discrepancy in the numbers of reads | unassigned | | I don't see any discrepancy in the number of reads, perhaps this can be removed? ​ |  
 +| Fastqc/​kmergenie on SeqPrepped data | unassigned | waiting on previous steps | |  
 +| End trim SeqPrepped data | Hussain | | |  
 +| 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 ​|  
 +| Plot contig size histogram for current assembly (SOAPdenovo2 results) | Markello | Complete ​| | 
 +| Plot scaffold size histogram for current assembly (SOAPdenovo2 results) | Markello | Complete ​| |
 | Find cost of creating a tagmentase library| Dudek | | ~$50 | | Find cost of creating a tagmentase library| Dudek | | ~$50 |
-| Merge/trim new data (SeqPrep) | Hussain | in progress ​| | +| Merge/trim new data (SeqPrep) | Hussain | Completed ​See wiki page for each data set for details ​
-| Analyze new data (preqc) | Richardson | In progress ​| |  +| Analyze new data (preqc) | Richardson | Completed | See wiki page for each data set for details |  
 +| Preqc on new mate pair SW041 SW042| Saremi | Completed | | 
 +| Update the wiki to include mate pair meta data | Eisenhart | completed |  
 +| Install CEGMA dependencies | Markello | Completed | Issue discovered: glib required for complete installation of latest version of genewise (CEGMA dependency) on head node, will use current installation of genewise. | 
 +| Create a file containing contigs longer than 5kb | Eisenhart | completed | file is here /​campusdata/​BME235/​S15_assemblies/​DiscovarDeNovo/​UCSF50%run/​bigContigs.fa | 
 +| Plot scaffold size histogram for current assembly (Discovar de novo results) | Dudek | Completed | 10% and the new UCSF 50% are up on the discovar team page | 
 +| Map lucigen mates against scaffolds | Dudek | completed ​See sam file at /​campusdata/​ndudek/​mapping_lucigen/​5kb_plus_discovar/​IJS8_mates_vs_discovar_bigContigs_5000.sam ​|
 | Analyze new data (fastqc) | Saremi |Completed | /​campusdata/​BME235/​S15_assemblies/​SOAPdenovo2/​Fastqc/​UCSF_BS-MK_fastqc /​campusdata/​BME235/​S15_assemblies/​SOAPdenovo2/​Fastqc/​UCSF_BS-tag_fastqc |  ​ | Analyze new data (fastqc) | Saremi |Completed | /​campusdata/​BME235/​S15_assemblies/​SOAPdenovo2/​Fastqc/​UCSF_BS-MK_fastqc /​campusdata/​BME235/​S15_assemblies/​SOAPdenovo2/​Fastqc/​UCSF_BS-tag_fastqc |  ​
-| Analyze SeqPrep results | | | |  
-| Error Correction new data| McGovern (Musket) & Richardson (BLESS/​racer) | In progress | These programs have not yet been run succesfully... | 
 | Adapter trim UCSF SW018 and SW019 libraries (skewer), remove duplicates (fastUniq)| Chaves & Dudek | Completed |/​campusdata/​BME235/​S15_assemblies/​DiscovarDeNovo/​UCSF_reads (Read 1 Sequencing Primer: 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT 3'; Read 2 Sequencing Primer: 5' GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT 3)| | Adapter trim UCSF SW018 and SW019 libraries (skewer), remove duplicates (fastUniq)| Chaves & Dudek | Completed |/​campusdata/​BME235/​S15_assemblies/​DiscovarDeNovo/​UCSF_reads (Read 1 Sequencing Primer: 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT 3'; Read 2 Sequencing Primer: 5' GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT 3)|
-Install bowtie ​Chaves ​Completed ​|/campusdata/​gchaves/Bowtie/​bowtie2-2.2.5+|SSpace on discovar de novo assembly fasta Eisenhart ​Complete ​Results are posted here , https://banana-slug.soe.ucsc.edu/​team_5_page:​sspacesummaryfile ​|  
-Install CEGMA dependencies ​Markello ​In progress ​Relying on IT to fix issues with completing compilation of wise2 (genewise) package which CEGMA requires ​|+Map reads against 2012 mitochondrion assembly ​Dudek Completed for UCSF SW018 and SW019 reads I did the mapping both for adapter-trimmed and adapter-trimmed & duplicate-free reads. The sam files are available at: /​campusdata/​BME235/​mitochondrion ​| 
archive/specific_task.txt · Last modified: 2015/08/04 03:32 by 68.180.228.52