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Diffstat (limited to 'tasks/felixl.gmi')
| -rw-r--r-- | tasks/felixl.gmi | 105 |
1 files changed, 101 insertions, 4 deletions
diff --git a/tasks/felixl.gmi b/tasks/felixl.gmi index 347f387..7a472a1 100644 --- a/tasks/felixl.gmi +++ b/tasks/felixl.gmi @@ -41,7 +41,7 @@ * PhD tasks * [ X ] Complete and share concept note and timeline to supervisors, have a meeting for progress - * [ ] Make a milestone on chapter one manuscript (deep dive into the selected papers){THE BIG PICTURE; a complete draft by early May} + * [+] Make a milestone on chapter one manuscript (deep dive into the selected papers){THE BIG PICTURE; a complete draft by early May} * Programming * [ ] Make a milestone with the uploader (really push and learn!) @@ -116,9 +116,106 @@ * [X] - document the new findings about smoothing using bcftools and plink * ## this week (09-06-onwards) -* [ ] - identify start and end points for haplotypes in hs genotype files -* [ ] - upload the final updates to gn2, test and see the results -* [ ] - gn-uploader/uploader folder, explore +* [+] - identify start and end points for haplotypes in hs genotype files +* [+] - upload the final updates to gn2, test and see the results +* [-] - gn-uploader/uploader folder, explore + +* ## this week (16-06-onwards) +* [X] - hs rats proximal and distal haplotype edges +* [+] - uploading kilifish using the backend route + +* ## this week (23-06-onwards) +* [X] - hs rats recombination counts +* [+] - kilifish to gn2 via backend + +* ## this week (30-06-onwards) +* [ ] - mapping offsprings to founders (hs rats) +* [ ] - upload kilifish to genenetwork +* [ ] - revise celegans smoothing (genotypes) + +* ## this week (07-07-onwards) +* [X] - generate haplotypes for offsprings and founders combined; intepretation next.., +* [+] - keep improving the uploader via data uploading and error solving +* [-] - close smoothing revision for celegans, as left before +* [X] - why should people read my paper on improving genotyping methods? +* - on smoothing (low density genotypes for mapping, high density genotypes for fine mapping.,) +* - liftovers due to reference versions (currently, a challenge to be looked upon) +* - founders and their offsprings in genotyping +* - pangenomics and machine learning for improved genotyping + +** keys (+; in progress, X; done, -; not yet) +* ## this week (14-07-onwards) +* [+] - map founders to offspring, work with only pure recombiantions + [+] - tools available? (plink, rqtl2, beagle, etc) + [+] - custom pipeline, to reflect gaps in the existing tools? (dealing with multiparent species) + [+] - documentation for the paper write up + +* ## this week (21-07-onwards) +* [ ] - HS rats smoothing continues +* [ ] - documenting the milestones +* [ ] - see the possibility to write a tool from it +* [ ] - Pushing kilifish to genenetwork2/learn the source code build up +* [ ] - resmoothen celegans genotypes with the new knowledge + +* ## this week (28-07-onwards) +* [-] - predict genotype probabilities with rqlt2 functions + - problems with control setup to load in the needed files for the functions +* [+] - comparison models for @individual rat vs 8 founders (similarities and percentage composition) + [+] - ongoing discussion with alex, there's progress + +* ## this week (04-08-onwards) +* [+] - Testing the logic to infer Hs outbred genotypes with the founders + - Managed to identify parents of origin for each snp on each rat per position, corresponding to the 8 founders + - Still, need to filter in the disntictive snps, then generate haplo blocks., + +* ## this week (11 - 08 - onwards) +* [X] - generate final haplo file and document +* [+] - testing on local gemma and in gn2 + +* ## this week (18-08-onwards) +* [+] - push for the file to be in gn2, and feedback from the team +* [X] - complete the local gemma run, interpret the results +* [+] - process the rest of the Xsomes for a ready file to go to gn2 +* - issues: over filtering snps, neglecting the one parent of origin, takes long to run. +* [+] - prepare an abstract for CTC conference in Barcelona + +* ## this week (01-09-onWards) +* [ ] - finetune abstract +* - include more of what i achieved: main focus; genotype smoothing on models with complex traits +* - thought map: generate plots, compare before and after smoothing, check for overlaps, and whether or not the peaks in traits are same before and after smoothing +* [ ] - troubleshoot inferring scripts for all Xsomes +* - request bonz/alex's help on this (to save time) + + +* ## this week (30-06-onwards) +* [X] - mapping offsprings to founders (hs rats) +* [+] - upload kilifish to genenetwork +* [-] - revise celegans smoothing (genotypes) + +* ## this week (07-07-onwards) +* [X] - generate haplotypes for offsprings and founders combined; intepretation next.., +* [+] - keep improving the uploader via data uploading and error solving +* [-] - close smoothing revision for celegans, as left before +* [X] - why should people read my paper on improving genotyping methods? +* - on smoothing (low density genotypes for mapping, high density genotypes for fine mapping.,) +* - liftovers due to reference versions (currently, a challenge to be looked upon) +* - founders and their offsprings in genotyping +* - pangenomics and machine learning for improved genotyping + +** keys (+; in progress, X; done, -; not yet) +* ## this week (14-07-onwards) +* [+] - map founders to offspring, work with only pure recombiantions + [+] - tools available? (plink, rqtl2, beagle, etc) + [+] - custom pipeline, to reflect gaps in the existing tools? (dealing with multiparent species) + [+] - documentation for the paper write up + +* ## this week (21-07-onwards) +* [ ] - HS rats smoothing continues +* [ ] - documenting the milestones +* [ ] - see the possibility to write a tool from it +* [ ] - Pushing kilifish to genenetwork2/learn the source code build up +* [ ] - resmoothen celegans genotypes with the new knowledge + ### Later weeks (non-programming tasks) |