Commit 8f1ea0b6 authored by Olivier Rue's avatar Olivier Rue
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metabarfood advances

parent a778b254
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...@@ -49,7 +49,7 @@ options(DT.options = list(pageLength = 10, ...@@ -49,7 +49,7 @@ options(DT.options = list(pageLength = 10,
buttons = c('copy', 'csv', 'excel', 'pdf', 'print'))) buttons = c('copy', 'csv', 'excel', 'pdf', 'print')))
``` ```
# MEAT
```{bash, eval=F} ```{bash, eval=F}
# Genologin # Genologin
...@@ -58,22 +58,34 @@ sh dada2_frogs.sh ...@@ -58,22 +58,34 @@ sh dada2_frogs.sh
``` ```
```{bash, eval=F} ```{bash, eval=F}
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS1/frogs.biom REAL/ITS1.biom #scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS1/frogs.biom MEAT/ITS1.biom
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS2/frogs.biom REAL/ITS2.biom #scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS2/frogs.biom MEAT/ITS2.biom
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/D1D2/frogs.biom REAL/D1D2.biom #scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/D1D2/frogs.biom MEAT/D1D2.biom
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/RPB2/frogs.biom REAL/RPB2.biom scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/RPB2/frogs.biom MEAT/RPB2.biom
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS1/frogs.tsv REAL/ITS1.tsv #scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS1/frogs.tsv MEAT/ITS1.tsv
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS2/frogs.tsv REAL/ITS2.tsv #scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS2/frogs.tsv MEAT/ITS2.tsv
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/D1D2/frogs.tsv REAL/D1D2.tsv #scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/D1D2/frogs.tsv MEAT/D1D2.tsv
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/RPB2/frogs.tsv REAL/RPB2.tsv scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/RPB2/frogs.tsv MEAT/RPB2.tsv
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS1/multiaff.tsv REAL/ITS1_multiaff.tsv #scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS1/multiaff.tsv MEAT/ITS1_multiaff.tsv
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS2/multiaff.tsv REAL/ITS2_multiaff.tsv #scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS2/multiaff.tsv MEAT/ITS2_multiaff.tsv
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/D1D2/multiaff.tsv REAL/D1D2_multiaff.tsv #scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/D1D2/multiaff.tsv MEAT/D1D2_multiaff.tsv
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/RPB2/multiaff.tsv REAL/RPB2_multiaff.tsv scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/RPB2/multiaff.tsv MEAT/RPB2_multiaff.tsv
``` ```
## Preparation of final BIOM files {.tabset}
### ITS1
### ITS2
### D1D2
### RPB2
## Analysis
```{r, eval=F} ```{r, eval=F}
if (!file.exists("REAL/ITS1.rds")) { if (!file.exists("REAL/ITS1.rds")) {
biomfile <- "REAL/ITS1.biom" biomfile <- "REAL/ITS1.biom"
...@@ -205,4 +217,46 @@ p + facet_grid(". ~ Marker", scales = "free_x", space = "free") ...@@ -205,4 +217,46 @@ p + facet_grid(". ~ Marker", scales = "free_x", space = "free")
```{r, eval=T} ```{r, eval=T}
p <- plot_composition(physeq = all, taxaRank1 = "Kingdom", taxaSet1 = "Fungi", taxaRank2 = "Species", numberOfTaxa = 22, x = "Sample") p <- plot_composition(physeq = all, taxaRank1 = "Kingdom", taxaSet1 = "Fungi", taxaRank2 = "Species", numberOfTaxa = 22, x = "Sample")
p + facet_grid(". ~ Marker", scales = "free_x", space = "free") p + facet_grid(". ~ Marker", scales = "free_x", space = "free")
``` ```
\ No newline at end of file
# CHEESE
```{bash, eval=F}
# Genologin
cd /work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/scripts
sh dada2_frogs.sh
```
```{bash, eval=F}
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/ITS1/frogs.biom CHEESE/ITS1.biom
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/ITS2/frogs.biom CHEESE/ITS2.biom
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/D1D2/frogs.biom CHEESE/D1D2.biom
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/RPB2/frogs.biom CHEESE/RPB2.biom
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/ITS1/frogs.tsv CHEESE/ITS1.tsv
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/ITS2/frogs.tsv CHEESE/ITS2.tsv
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/D1D2/frogs.tsv CHEESE/D1D2.tsv
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/RPB2/frogs.tsv CHEESE/RPB2.tsv
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/ITS1/multiaff.tsv CHEESE/ITS1_multiaff.tsv
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/ITS2/multiaff.tsv CHEESE/ITS2_multiaff.tsv
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/D1D2/multiaff.tsv CHEESE/D1D2_multiaff.tsv
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/RPB2/multiaff.tsv CHEESE/RPB2_multiaff.tsv
```
## Preparation of final BIOM files {.tabset}
### ITS1
### ITS2
### D1D2
### RPB2
## Analysis
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