Difference between revisions of "Hinxton 2016.01- Meeting minutes"
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* Lots of work on documentation | * Lots of work on documentation | ||
* ParaSite expresso - conversations with Caltech about setting this up | * ParaSite expresso - conversations with Caltech about setting this up | ||
+ | |||
+ | |||
+ | |||
+ | ==January 05, 2016 == | ||
+ | |||
+ | In attendance: KH, PD, GW, MP | ||
+ | |||
+ | === Curation === | ||
+ | |||
+ | * C. elegans | ||
+ | ** ncRNAS | ||
+ | *** Looked into classification in WormMine. Need to liaise with OICR to make sure right tag(s) being used as primary biotype | ||
+ | *** tRNAs | ||
+ | **** HelpDesk ticket on absence GGG (Proline)-antocodon tRNA in C. elegans. This is known (and true for many species). | ||
+ | **** Discussion with Todd Lowe on project to re-name tRNAs across human, fly to make consistent. Should worm be included. | ||
+ | ** RNASeq introns | ||
+ | *** Separation of RNASeq introns by score (<1000 reads, >1000 reads), making it easier to see "high confidence" introns in Fmap | ||
+ | ** Continued curation of genes with CGC names | ||
+ | * B. malayi | ||
+ | ** Remapping of TIGR models to new V4 assembly. Should help with gene name mapping | ||
+ | ** Amendments to life-stage ontology | ||
+ | ** New RNASeq libraries curated and aligned, ready for WS253 | ||
+ | ** Continue to chase why V3 assembly STILL not correct in ENA/NCBI | ||
+ | |||
+ | === Development / Production === | ||
+ | |||
+ | * Trinity pipeline | ||
+ | ** Comparison of results using different input data sets | ||
+ | * QC checks in build | ||
+ | ** Calculation of statistics at key checkpoints in the build | ||
+ | *** This is already in place, but we should make it more robust | ||
+ | * Assembly Hub | ||
+ | ** WS252 hub built. New Brugia assembly seems to have been handled correctly | ||
+ | * Ensembl Genomes 31 | ||
+ | ** We need to do compara production for this (next week) | ||
+ | |||
+ | === General === | ||
+ | |||
+ | * Started preparation of SAB talks |
Latest revision as of 13:18, 15 January 2016
Contents
January 08, 2016
In attendance: KH, PD, GW, BB, JL
Curation
- Reviewing "known" genes with poor gene models
- PD and GW reviewing genes with a GCG name but questionable gene model
- Many/most of these are members of gene families.
- Work has involved (and continues to involve) structure changes, new isoforms, and re-classification of CDSs as pseusogenes
- Review of some CDSs models based on lincRNA data from David Greenstein (U. Minnesota)
- Comprehensive re-annotation of hlb-1 locus (based on feedback from a researcher from Penn state university)
Development
- New infrastructure for curating RNASeq meta data
- Ini file under version control, maintained by a combination of scripts and manual curation
- Will be a input to a script that generates the Track Hub (labelling tracks correctly etc)
- Continued work on using Trinity to "distill" RNASeq data for use in UTR addition to coding models
ParaSite
- Release 5 due soon
- BioMart currently being build
- Full testing will be done early next week
- Focus on C. elegans, and two new assemblies (E. multicularis and H. microstoma)
- Starting to look into Biomart alternatives (elastic search)
- ParaSite talk at the EG SAB
- Lots of work on documentation
- ParaSite expresso - conversations with Caltech about setting this up
January 05, 2016
In attendance: KH, PD, GW, MP
Curation
- C. elegans
- ncRNAS
- Looked into classification in WormMine. Need to liaise with OICR to make sure right tag(s) being used as primary biotype
- tRNAs
- HelpDesk ticket on absence GGG (Proline)-antocodon tRNA in C. elegans. This is known (and true for many species).
- Discussion with Todd Lowe on project to re-name tRNAs across human, fly to make consistent. Should worm be included.
- RNASeq introns
- Separation of RNASeq introns by score (<1000 reads, >1000 reads), making it easier to see "high confidence" introns in Fmap
- Continued curation of genes with CGC names
- ncRNAS
- B. malayi
- Remapping of TIGR models to new V4 assembly. Should help with gene name mapping
- Amendments to life-stage ontology
- New RNASeq libraries curated and aligned, ready for WS253
- Continue to chase why V3 assembly STILL not correct in ENA/NCBI
Development / Production
- Trinity pipeline
- Comparison of results using different input data sets
- QC checks in build
- Calculation of statistics at key checkpoints in the build
- This is already in place, but we should make it more robust
- Calculation of statistics at key checkpoints in the build
- Assembly Hub
- WS252 hub built. New Brugia assembly seems to have been handled correctly
- Ensembl Genomes 31
- We need to do compara production for this (next week)
General
- Started preparation of SAB talks