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--- archive:specific_task [2015/05/12 16:37]
ceisenhart
+++ archive:specific_task [2015/06/01 19:22]
jdhouser
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 |Task| Assignee | Status | Notes|
-| Plot contig size vs total genome size for assemblies | | | |
+|Install Maker| Houser | In progress | Working on getting dependencies installed |
-| Ask UCSF about the discrepancy in the numbers of reads | | | I don't see any discrepancy in the number of reads, perhaps this can be removed?  |
+|Assemble repeat genome with RepArk|Team 1|In progress|Charles has started a test run using the original Hiseq and Miseq reads|
-| Analyze SeqPrep results | | | |
+|Run GapCloser on SOAP denovo assembly|Charles|In progress| Use SOAP denovo's external gap closer. Chose a reasonable name for new assembly. |
-| Preqc on new mate pair SW041 SW042| | | |
+|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 histogram for current assembly (SOAPdenovo2 results) | Markello | In progress | |
+| Mate-pair adapter and linker removal|  | | |
-| Plot scaffold size histogram for current assembly (SOAPdenovo2 results) | Markello | In progress | |
+| Measuring insert size for each mate-pair library | unassigned | | |
-| Find cost of creating a tagmentase library| Dudek | | ~$50 |
+| Making Seqprep, adapter removed, end-trimmed library files | unassigned | | |
-| Merge/trim new data (SeqPrep) | Hussain | in progress | |
+| Blast long contigs and analyze results | unassigned| | Check the browser for the 30 longest contigs from each group with contigs|
-| Analyze new data (preqc) | Richardson | In progress | |
+| 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 |
-| Error Correction new data| McGovern (Musket) & Richardson (BLESS/racer) | In progress | These programs have not yet been run succesfully... |
+| 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 |
+| Merge/trim new data (SeqPrep) | Hussain | Completed | See wiki page for each data set for details |
+| 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 | In progress | Relying on IT to fix issues with completing compilation of wise2 (genewise) package which CEGMA requires |
+| 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 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 ~220bp, compared to an expected read length of 300bp and insert size over 1kb. Also, I spoke with Brendan and there is new mate-pair data coming soon (expected the week of May 10th). |
+| 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 |
 | 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)|
-|SSpace on discovar de novo assembly fasta | Eisenhart | In process | queued |
+|SSpace on discovar de novo assembly fasta | Eisenhart | Complete | Results are posted here , https://banana-slug.soe.ucsc.edu/team_5_page:sspacesummaryfile |
+| 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 |

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