SCHEDULED: <2023-10-07 Sat>
- [1/5] <[Culture]> - https://scut.srht.site/notes/medecine/20230528235124-culture.html
- [1/5] <[Syphilis]> - "~/annex/public/lessons/microbiologie/bacterio/Syphilis.pdf"

      - [1/5] <(Angines)>
- [1/5] <(ATBg Enterobacteries)>
- [1/5] <(ATBg staphylocoques)>
- [1/5] <(ATBg streptococque, entérocoque, Listeria)>
- [1/5] <(ATBg)>
- [1/5] <(Angines)>
- [1/5] <(Cambylobacter)>
- [1/5] <(Chlamydia, mycoplasme)>
- [1/5] <(Clostridium difficile)>
- [1/5] <(Concentrations critiques)>
- [1/5] <(Conseil anti-infectieux)>
- [1/5] <(Culture)>
- [1/5] <(Declaration obligatoire)>
- [1/5] <(Diagnostic moléculaire)>
- [1/5] <(EBCU etiologies)>
- [1/5] <(ECBU interpretation)>
- [1/5] <(ECBU pre-analytique)>
- [1/5] <(EEQ, CIQ)>
- [1/5] <(Examen microscopique)>
- [1/5] <(Gonocoque)>
- [1/5] <(Hemocultures 1)>
- [1/5] <(Hemocultures 2)>
- [1/5] <(Hygiène)>
- [1/5] <(Infections cutanees)>
- [1/5] <(Legionelle)>
- [1/5] <(MALDI)>
- [1/5] <(Meningites bacteriennes)>
- [1/5] <(Moleculaire)>
- [1/5] <(Pré-analytique)>
- [1/5] <(Qualité)>
- [1/5] <(Salmonelle)>
- [1/5] <(Securite Transfusionnelle)>
- [1/5] <(Serologie bacterienne)>
- [1/5] <(Syphilis)>
- [1/5] <(Tests rapides)>
- [1/5] <(Tuberculose)>
- [1/5] <(Typage moléculaire)>
- [1/5] <(Vaccination personnel)>

- [1/5] <[ATBg staphylocoques]> - "~/annex/public/lessons/microbiologie/bacterio/Antibiogramme - Staphylocoques.pdf"
- [1/5] <[ATBg streptococque, entérocoque, Listeria]> - "~/annex/public/lessons/microbiologie/bacterio/Antibiogramme - Streptococoque, enterocoque, Listeria.pdf"
- [1/5] <[Chlamydia, mycoplasme]> - "~/annex/public/lessons/microbiologie/bacterio/Chlamydia - mycoplasmes.pdf"
- [1/5] <[Moléculaire (bactério)]> - "~/annex/public/lessons/microbiologie/bacterio/Diagnostic moleculaire - Bacteriologie.pdf"
- [1/5] <[EBCU etiologies]> - "~/annex/public/lessons/microbiologie/bacterio/EBCU etiologies.pdf"
- [1/5] <[ECBU interpretation]> - "~/annex/public/lessons/microbiologie/bacterio/ECBU interpretation.pdf"
- [1/5] <[ECBU pre-analytique]> - "~/annex/public/lessons/microbiologie/bacterio/ECBU pre-analytique.pdf"
- [1/5] <[EEQ, CIQ]> - "~/annex/public/lessons/microbiologie/bacterio/EEQ, CIQ.pdf"
- [1/5] <[Examen microscopique]> - "~/annex/public/lessons/microbiologie/bacterio/Examen microscopique.pdf"
- [1/5] <[Gonocoque]> - "~/annex/public/lessons/microbiologie/bacterio/Gonocoque.pdf"
- [1/5] <[Hygiène]> - "~/annex/public/lessons/microbiologie/bacterio/Hygiène.pdf"
- [1/5] <[Infections cutanees]> - "~/annex/public/lessons/microbiologie/bacterio/Infections cutanees.pdf"
- [1/5] <[MALDI - TOF]> - "~/annex/public/lessons/microbiologie/bacterio/MALDI - TOF.pdf"
- [1/5] <[Pre-analytique microbiologie/bacteriologie]> - "~/annex/public/lessons/bacterio/Pre-analytique bacteriologie.pdf"
- [1/5] <[Qualite]> - "~/annex/public/lessons/microbiologie/bacterio/Qualite.pdf"
- [1/5] <[Securite Transfusionnelle]> - "~/annex/public/lessons/microbiologie/bacterio/Securite Transfusionnelle.pdf"
- [1/5] <[Serologie bacterienne]> - "~/annex/public/lessons/microbiologie/bacterio/Serologie bacterienne.pdf"
- [1/5] <[Tests rapides antigeniques et moleculaires]> - "~/annex/public/lessons/microbiologie/bacterio/Tests rapides antigeniques et moleculaires.pdf"
- [1/5] <[Tuberculose]> - "~/annex/public/lessons/microbiologie/bacterio/Tuberculose.pdf"
- [1/5] <[Moleculaire]> - "~/annex/public/lessons/microbiologie/bacterio/Typage moleculaire bacterien.pdf"
- [1/5] <[Vaccination personnel]> - "~/annex/public/lessons/microbiologie/bacterio/Vaccination personnel.pdf"
- [1/5] <[Angines]> - "~/annex/public/lessons/microbiologie/bacterio/Angines bacteriennes.pdf"
- [1/5] <[ATBg Enterobacteries]> - "~/annex/public/lessons/microbiologie/bacterio/Antibiogramme - Enterobacteries.pdf"
- [1/5] <[ATBg]> - "~/annex/public/lessons/microbiologie/bacterio/Antibiogramme.pdf"
- [1/5] <[Cambylobacter]> - "~/annex/public/lessons/microbiologie/bacterio/Cambylobacter.pdf"
- [1/5] <[Clostridium difficile]> - "~/annex/public/lessons/microbiologie/bacterio/Clostridium difficile.pdf"
- [1/5] <[Concentrations critiques]> - "~/annex/public/lessons/microbiologie/bacterio/Concentrations critiques.pdf"
- [1/5] <[Conseil anti-infectieux]> - "~/annex/public/lessons/microbiologie/bacterio/Conseil anti-infectieux.pdf"
- [1/5] <[Declaration obligatoire]> - "~/annex/public/lessons/microbiologie/bacterio/Declaration obligatoire.pdf"
- [1/5] <[Hemocultures 1]> - "~/annex/public/lessons/microbiologie/bacterio/Hemocultures 1.pdf"
- [1/5] <[Hemocultures 2]> - "~/annex/public/lessons/microbiologie/bacterio/Hemocultures 2.pdf"
- [1/5] <[Legionelle]> - "~/annex/public/lessons/microbiologie/bacterio/Legionelle.pdf"
- [1/5] <hMeningites bacteriennes ]> - "~/annex/public/lessons/microbiologie/bacterio/Meningites bacteriennes .pdf"
- [1/5] <[Salmonelle - shigelle]> - "~/annex/public/lessons/microbiologie/bacterio/Salmonelle - shigelle.pdf"

*** TODO Traitement patients bouches
SCHEDULED: <2023-10-07 Sat>
*** TODO Faire analyse selles
SCHEDULED: <2023-10-07 Sat>

*** DONE Traitement patients bouches
CLOSED: [2023-10-07 Sat 18:01] SCHEDULED: <2023-10-07 Sat>
*** DONE Faire analyse selles
CLOSED: [2023-10-07 Sat 19:30] SCHEDULED: <2023-10-07 Sat>
:LOGBOOK:
CLOCK: [2023-10-07 Sat 18:02]--[2023-10-07 Sat 19:30] =>  1:28
:END:
*** TODO Revoir avec Audrey pour différence (bleu et jaune)
SCHEDULED: <2023-10-12 Thu>
*** TODO Réunion audrey
SCHEDULED: <2023-10-12 Thu>

SCHEDULED: <2023-10-07 Sat>
*** TODO Présenter Torres 2022

SCHEDULED: <2023-10-09 Mon>
*** TODO [#A] Présenter Torres 2022 "~/papers/bacterio/torres2022.pdf"

** TODO Remplacer clavier SK :clavier:
/Entered on/ [2023-10-07 Sat 22:58]
*** WAIT Demande à Cooler Master un remplacement
SCHEDULED: <2023-10-15 Sun>
Envoyée <2023-10-07 Sat>
Sera probablement refusée car via Amazon
*** TODO Demande Amazon si Cooler master refuse
SCHEDULED: <2023-10-14 Sat>
Renvoie vers le constructeur ...

SCHEDULED: <2023-10-08 Sun>

SCHEDULED: <2023-10-11 Wed>

** TODO Résilier eau
SCHEDULED: <2023-10-25 Wed>
** TODO Résilier électricité
SCHEDULED: <2023-10-25 Wed>

SCHEDULED: <2023-10-07 Sat>

SCHEDULED: <2023-10-14 Sat>

LED: <2023-10-10 Tue>
**** DONE En T2T avec liftover (filtre = spip) : ok mais lent et trop de variants :tests:
CLOSED: [2023-09-17 Sun 17:13] SCHEDULED: <2023-09-17 Sun>
1. Conversion en bed
#+begin_src sh :dir:~/code/sanger
open snvs-cento-sanger.csv | select chrom pos | insert pos2 {$in.pos } | to csv --separator="\t" | save snvs-cento-sanger.bed -f
#+end_src
2. Liftover avec UCSC (en ligne)
NB: vérifié sur le premier résultat en cherche le read contenant le variant (samtools view -r puis samtools view | grep en T2T) et avec l'aide d'IGV, on a un variant qui correspond en
chr1:10757746
3. En supposant que l'ordre des variants n'a pas changé, on ajoute simplement REF et ALT avec annotateLifted.jl
Annotation spip *très lente* : 1h13 !
Résultat:
2×3 DataFrame
 Row │ variant              meanQual  depth
     │ String               Float64   Int64
─────┼──────────────────────────────────────
   1 │ chr12:g.13594572      60.0      1
   2 │ chr17:g.10204026      60.0      1
144 found over 146
filter depth : another 0 missed variants
filter poly : another 0 missed variants
filter vep   : another 0 missed variants
Et on a trop de variants en sortie (7330 !)
**** DONE Mail Paul avec résultats filtre en T2T + nouveau schéma
CLOSED: [2023-09-17 Sun 23:15] SCHEDULED: <2023-09-17 Sun>
* Ré-interprétation
** PROJ Lancer tests sur données brutes [167/250] <(samples.csv)>  <(runs.waiting)>
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- [ ] 2200622355_63030956
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- [ ] 2300232688_63130821
- [ ] 2300292749_63109239
- [ ] 230029277_63109247
- [ ] 2300294712_63109236
- [ ] 2300308032_63111581
- [ ] 2300323537_63114209
- [ ] 2300334609_63115535
- [ ] 2300346867_63118093
- [ ] 2300346867_63118093_NA12878
- [ ] 2300348940_63118099
- [ ] 2300359806_63119915
- [ ] 2300380476_63123963
- [ ] 2300382582_63123749
- [ ] 2300384269_63126867
- [ ] 2300407581_63130826
- [ ] 2300407626_63130842
- [ ] 2300409593_63130874
- [ ] 2300409612_63130980
- [ ] 2300417623_63131524
** TODO Variants manqués
*** TODO 63012582: chr10:g.102230760
*** TODO 63060439: chr15:g.26869324 = Problème de profondeur DP=15
SCHEDULED: <2023-10-08 Sun>
GT:AD:DP:GQ:PL 0/1:9,6:15:99:103,0,213
* Résultats
** TODO Speed-up BWA-mem
SCHEDULED: <2023-10-08 Sun>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-10-08 Sun>
* Communication
** DONE Mail NGS-diag
CLOSED: [2023-10-06 Fri 08:04] SCHEDULED: <2023-10-06 Fri>
/Entered on/ [2023-10-04 Wed 19:33]


"projects.org"
("ATBg_Enterobacteries" nil nil link-to-file ("/home/alex/annex/public/lessons/microbiologie/bacterio/Antibiogramme - Enterobacteries.pdf" t) "alex@gentoo" "20231008:10:30:00" nil nil)
("ATBg_staphylocoques" nil nil link-to-file ("/home/alex/annex/public/lessons/microbiologie/bacterio/Antibiogramme - Staphylocoques.pdf" t) "alex@gentoo" "20231008:10:30:00" nil nil)
("ATBg_streptococque,_entérocoque,_Listeria" nil nil link-to-file ("/home/alex/annex/public/lessons/microbiologie/bacterio/Antibiogramme - Streptococoque, enterocoque, Listeria.pdf" t) "alex@gentoo" "20231008:10:30:00" nil nil)
("ATBg" nil nil link-to-file ("/home/alex/annex/public/lessons/microbiologie/bacterio/Antibiogramme.pdf" t) "alex@gentoo" "20231008:10:30:00" nil nil)
("Angines" nil nil link-to-file ("/home/alex/annex/public/lessons/microbiologie/bacterio/Angines bacteriennes.pdf" t) "alex@gentoo" "20231008:10:30:00" nil nil)
("Antibiogramme" nil nil link-to-file ("/home/alex/home/alex/annex/public/lessons/microbiologie/bacterio/Antibiogramme.pdf" t) "alex@gentoo" "20231007:10:18:41" nil nil)
("Cambylobacter" nil nil link-to-file ("/home/alex/annex/public/lessons/microbiologie/bacterio/Cambylobacter.pdf" t) "alex@gentoo" "20231008:10:30:00" nil nil)
("Chlamydia,_mycoplasme" nil nil link-to-file ("/home/alex/annex/public/lessons/microbiologie/bacterio/Chlamydia - mycoplasmes.pdf" t) "alex@gentoo" "20231008:10:30:00" nil nil)
("Clostridium_difficile" nil nil link-to-file ("/home/alex/annex/public/lessons/microbiologie/bacterio/Clostridium difficile.pdf" t) "alex@gentoo" "20231008:10:30:00" nil nil)
("Concentrations_critiques" nil nil link-to-file ("/home/alex/annex/public/lessons/microbiologie/bacterio/Concentrations critiques.pdf" t) "alex@gentoo" "20231008:10:30:00" nil nil)
("Conseil_anti-infectieux" nil nil link-to-file ("/home/alex/annex/public/lessons/microbiologie/bacterio/Conseil anti-infectieux.pdf" t) "alex@gentoo" "20231008:10:30:00" nil nil)
("Culture" nil nil www-url ("https:/scut.srht.site/notes/medecine/20230528235124-culture.html") "alex@gentoo" "20231007:20:16:54" nil nil)
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