On as commencer par FROGS avec le script suivant
Script dans le dossier "./Run_Frogs/run3"
Script - FROGS
To improve confidence in the taxonomy, we also manually corrected 107 affiliations that had a percentage of coverage less than 100% and / or a percentage of identity inferior to 97%.
In this screening, we used the following rules.
First, when the percentage of identity was inferior to 90% or if the percentage of coverage was inferior to 95%, we deleted the taxonomy.
Second a minimum percentage of identity to keep a specific taxonomic rank was applied: 97% for species, 95% for genus, 90% for family.
Third, we verified that the RDP classifier gave the same taxonomy with a bootstrap superior of 0.9.
Tout d'abords, l'analyse de FastQC et de FROGS pour FS et HS
Script FS dans le dossier "./R_notebook/Food_Stress/FS\ -\ FastQC\ et\ Prepro/"
Script - Food Stress - FastQC et Frogs
HTML - Food Stress - FastQC et Frogs
Script HS dans le dossier "./R_notebook/Heat_Stress/HS\ -\ FastQC\ et\ Prepro/"
Script - Heat Stress - FastQC et Frogs
HTML - Heat Stress - FastQC et Frogs
Tout d'abord on fais le filtre a 50%
Script Filtre dans "./R_notebook/Trim_OTU/Filtre\ a\ 50%/"
Script - Description du Filtre a 50%
HTML - Description du Filtre a 50%
J'avais aussi tester un filtre a 30%
Script Filtre dans "./R_notebook/Trim_OTU/Filtre\ a\ 30%/"
Script - Description du Filtre a 30%
HTML - Description du Filtre a 30%
Avant d'enlever les OTU, nous avons voulus tester OTU -> Outlier ou l'inverse
Script dans "./R_notebook/Trim_OTU/OTU_Outlier\ et\ Outlier_OTU/"
Script - OTU -> Outlier
HTML - OTU -> Outlier
Script - Outlier -> OTU
HTML - Outlier -> OTU
Puis on enlève les OTU
Script outlier dans "./R_notebook/Trim_OTU/Outlier\ Final/"
Script - Outlier, the final solution !
HTML - Outlier, the final solution !
Donc on fais les analyses sur le Feed_Stress
Script dans "./R_notebook/Food_Stress/FS\ après\ Outlier/"
Script --- Food Stress - Analyse global
HTML --- Food Stress - Analyse global
Script --- Food Stress - Biologie
HTML --- Food Stress - Biologie
Script --- Food Stress - Analyse différentiel DESeq2
HTML --- Food Stress - Analyse différentiel DESeq2
Puis on finis par le Heat_Stress
Script dans "./R_notebook/Heat_Stress/HS\ après\ Outlier/"
Script --- Heat Stress - Analyse global
HTML --- Heat Stress - Analyse global
Script --- Heat Stress - Biologie
HTML --- Heat Stress - Biologie
Script --- Heat Stress - Analyse différentiel DESeq2
HTML --- Heat Stress - Analyse différentiel DESeq2
Enfin voici le script fais pour le rapport de stage avec FS et HS
Script dans "./R_notebook/Rapport_de_stage/"
Script --- FS et HS Rapport de stage