* <2023-08-15 Tue> Running
Sprint: 8x40s, 2min repos

** TODO Demande remboursement frais compte bancaire
SCHEDULED: <2023-08-13 Sun 18:00>

** WAIT Demande remboursement frais compte bancaire

anger :xamscissors:
**** DONE Générer la liste
CLOSED: [2023-08-13 Sun 22:26] SCHEDULED: <2023-08-13 Sun 12:00>
**** TODO 2 variants chr20 dans NA12878 avec XAMscissors
SCHEDULED: <2023-08-13 Sun 13:00>
***** DONE Insertion
CLOSED: [2023-08-13 Sun 23:31] SCHEDULED: <2023-08-13 Sun>
On récupère le BAM
#+begin_src sh :dir /home/alex/code/bisonex/out
scp /Work/Users/apraga/bisonex/out/HG002-151002_7001448_0359_AC7F6GANXX-GRCh38/preprocessing/mapped/HG002-151002_7001448_0359_AC7F6GANXX-GRCh38.bam
#+end_src
On formate les données
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
julia --project=.. formatXamscissors.jl
#+end_src
On génère les fastq
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
julia --project=.. xamscissors.jl
#+end_src
On upload
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
cd out
mv inserted_1.fq.gz HG002-sanger-inserted-chr20_1.fq.gz
mv inserted_2.fq.gz HG002-sanger-inserted-chr20_2.fq.gz
#+end_src
On upload
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
scp HG002-sanger-inserted-chr20_*.fq.gz meso:/Work/Users/apraga/bisonex/data/
#+end_src
Fichier de configuration
patient,sample,fastq1,fastq2
HG002,sanger-chr20,data/HG002-sanger-inserted-chr20_1.fq.gz,data/HG002-sanger-inserted-chr20_2.fq.gz
On lance la simulation
#+begin_src
nextflow run main.nf -profile standard,helios --input=samples-synthetic.csv --genome=GRCh38  -bg
#+end_src
***** DONE Vérifier post alignement
CLOSED: [2023-08-13 Sun 23:44] SCHEDULED: <2023-08-13 Sun>
***** TODO Vérifier haplotypecaller
SCHEDULED: <2023-08-13 Sun>
**** TODO Tout insérer dans NA12878 avec XAMscissors
SCHEDULED: <2023-08-14 Mon>
**** TODO Données simuscop 200x
SCHEDULED: <2023-08-22 Tue>
* Résultats
** TODO Speed-up BWA-mem
SCHEDULED: <2023-08-26 Sat>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-08-26 Sat>

anger :xamscissors:
**** DONE Générer la liste
CLOSED: [2023-08-13 Sun 22:26] SCHEDULED: <2023-08-13 Sun 12:00>
**** DONE 2 variants chr20 dans NA12878 avec XAMscissors
CLOSED: [2023-08-15 Tue 00:13] SCHEDULED: <2023-08-13 Sun 13:00>
***** DONE Insertion
CLOSED: [2023-08-13 Sun 23:31] SCHEDULED: <2023-08-13 Sun>
On récupère le BAM
#+begin_src sh :dir /home/alex/code/bisonex/out
scp /Work/Users/apraga/bisonex/out/HG002-151002_7001448_0359_AC7F6GANXX-GRCh38/preprocessing/mapped/HG002-151002_7001448_0359_AC7F6GANXX-GRCh38.bam
#+end_src
On formate les données
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
julia --project=.. formatXamscissors.jl
#+end_src
On génère les fastq
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
julia --project=.. xamscissors.jl
#+end_src
On upload
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
cd out
mv inserted_1.fq.gz HG002-sanger-inserted-chr20_1.fq.gz
mv inserted_2.fq.gz HG002-sanger-inserted-chr20_2.fq.gz
#+end_src
On upload
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
scp HG002-sanger-inserted-chr20_*.fq.gz meso:/Work/Users/apraga/bisonex/data/
#+end_src
Fichier de configuration
patient,sample,fastq1,fastq2
HG002,sanger-chr20,data/HG002-sanger-inserted-chr20_1.fq.gz,data/HG002-sanger-inserted-chr20_2.fq.gz
On lance la simulation
#+begin_src
nextflow run main.nf -profile standard,helios --input=samples-synthetic.csv --genome=GRCh38  -bg
#+end_src
***** DONE Vérifier post alignement
CLOSED: [2023-08-13 Sun 23:44] SCHEDULED: <2023-08-13 Sun>
***** DONE Vérifier haplotypecaller
CLOSED: [2023-08-15 Tue 00:13] SCHEDULED: <2023-08-13 Sun>
***** DONE Vérifier post-filtre
CLOSED: [2023-08-15 Tue 00:13]
**** TODO Tout insérer dans NA12878 avec XAMscissors
SCHEDULED: <2023-08-14 Mon>
**** TODO Données simuscop 200x
SCHEDULED: <2023-08-22 Tue>
* Résultats
** TODO Speed-up BWA-mem
SCHEDULED: <2023-08-26 Sat>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-08-26 Sat>