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Commit 400f564c authored by Cedric Midoux's avatar Cedric Midoux
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Shotgun metagenomics/analyses.Rmd
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......@@ -3,7 +3,7 @@ title: "Shotgun metagenomics"
author: "Valentin Loux - Cédric Midoux - Olivier Rué"
subtitle: "Migale facility"
css: css/styles.css
date: "2020/09/15"
date: "2021-06-25"
bibliography: biblio.bib
link-citations: yes
output:
......@@ -33,7 +33,7 @@ Créer cette arborescence votre espace `work`
TRAINING/
├── CLUSTER/
├── ANALYSES/
└── ANALYSES/
```{bash}
......@@ -220,7 +220,7 @@ Vérifiez que les fichiers FASTQ sont conformes et obtenez des statistiques sur
*Étape 1*: Trouver l'environnement conda de seqkit
```{bash}
conda info --envs |grep sekit
conda info --envs |grep seqkit
```
*Étape 2*: Lancer le module `stat` de l'outil seqkit sur tous les fichiers FASTQ
......@@ -767,17 +767,17 @@ cd ../
<summary>Sur le jeu de données réel</summary>
file format type num_seqs sum_len min_len avg_len max_len
METABAT/metabat.10.fa FASTA DNA 136 3,725,815 2,805 27,395.7 149,225
METABAT/metabat.1.fa FASTA DNA 40 205,248 2,744 5,131.2 7,133
METABAT/metabat.2.fa FASTA DNA 72 2,959,658 3,032 41,106.4 153,158
METABAT/metabat.3.fa FASTA DNA 73 669,163 3,104 9,166.6 12,922
METABAT/metabat.4.fa FASTA DNA 285 4,011,784 2,590 14,076.4 96,608
METABAT/metabat.5.fa FASTA DNA 355 1,219,472 1,680 3,435.1 8,355
METABAT/metabat.6.fa FASTA DNA 22 254,569 3,364 11,571.3 22,066
METABAT/metabat.7.fa FASTA DNA 205 877,763 2,502 4,281.8 8,101
METABAT/metabat.8.fa FASTA DNA 188 1,945,611 2,515 10,349 29,816
METABAT/metabat.9.fa FASTA DNA 77 3,968,889 2,833 51,544 244,528
METABAT/metabat.unbinned.fa FASTA DNA 2,466 4,896,175 1,000 1,985.5 84,317
METABAT/metabat.10.fa FASTA DNA 79 3,972,900 2,833 50,289.9 244,528
METABAT/metabat.1.fa FASTA DNA 305 1,043,115 1,680 3,420 8,355
METABAT/metabat.2.fa FASTA DNA 50 255,987 2,744 5,119.7 7,662
METABAT/metabat.3.fa FASTA DNA 290 1,565,251 2,502 5,397.4 29,816
METABAT/metabat.4.fa FASTA DNA 112 1,437,788 2,627 12,837.4 25,098
METABAT/metabat.5.fa FASTA DNA 52 2,282,155 2,920 43,887.6 116,560
METABAT/metabat.6.fa FASTA DNA 74 2,982,386 3,032 40,302.5 153,121
METABAT/metabat.7.fa FASTA DNA 69 656,990 3,491 9,521.6 17,523
METABAT/metabat.8.fa FASTA DNA 281 3,994,721 2,590 14,216.1 96,608
METABAT/metabat.9.fa FASTA DNA 81 1,424,958 2,805 17,592.1 26,447
METABAT/metabat.unbinned.fa FASTA DNA 2,521 5,095,982 1,000 2,021.4 84,317
</details>
......@@ -806,18 +806,17 @@ qsub -cwd -V -q formation.q -N checkm -o LOG -e LOG -b y "conda activate checkm-
| Bin Id | Marker lineage | # genomes | # markers | # marker sets | 0 | 1 | 2 | 3 | 4 | 5+ | Completeness | Contamination | Strain heterogeneity |
| :--------------: | :------------------------------: | :-------: | :-------: | :-----------: | :--: | :--: | :--: | :--: | :--: | :--: | :----------: | :-----------: | :------------------: |
| metabat.1 | root (UID1) | 5656 | 56 | 24 | 56 | 0 | 0 | 0 | 0 | 0 | 0.00 | 0.00 | 0.00 |
| metabat.2 | o__Pseudomonadales (UID4679) | 87 | 674 | 364 | 16 | 652 | 5 | 1 | 0 | 0 | 97.39 | 1.58 | 12.50 |
| metabat.3 | k__Bacteria (UID203) | 5449 | 104 | 58 | 98 | 6 | 0 | 0 | 0 | 0 | 3.45 | 0.00 | 0.00 |
| metabat.4 | c__Gammaproteobacteria (UID4444) | 263 | 506 | 232 | 16 | 479 | 11 | 0 | 0 | 0 | 94.65 | 3.79 | 63.64 |
| metabat.5 | f__Rhodobacteraceae (UID3340) | 84 | 568 | 330 | 410 | 156 | 2 | 0 | 0 | 0 | 27.20 | 0.45 | 0.00 |
| metabat.6 | root (UID1) | 5656 | 56 | 24 | 56 | 0 | 0 | 0 | 0 | 0 | 0.00 | 0.00 | 0.00 |
| metabat.7 | k__Bacteria (UID203) | 5449 | 104 | 58 | 86 | 18 | 0 | 0 | 0 | 0 | 25.34 | 0.00 | 0.00 |
| metabat.8 | k__Bacteria (UID203) | 5449 | 104 | 58 | 73 | 31 | 0 | 0 | 0 | 0 | 48.28 | 0.00 | 0.00 |
| metabat.9 | c__Gammaproteobacteria (UID4444) | 263 | 507 | 232 | 22 | 474 | 11 | 0 | 0 | 0 | 98.71 | 0.97 | 54.55 |
| metabat.10 | o__Rhizobiales (UID3447) | 356 | 416 | 249 | 14 | 308 | 4 | 0 | 0 | 0 | 82.13 | 1.20 | 0.00 |
| metabat.unbinned | k__Bacteria (UID203) | 5449 | 104 | 58 | 24 | 34 | 25 | 15 | 5 | 1 | 65.17 | 36.26 | 13.64 |
| metabat.1 | f__Rhodobacteraceae (UID3340) | 84 | 568 | 330 | 415 | 152 | 1 | 0 | 0 | 0 | 26.77 | 0.30 | 0.00 |
| metabat.2 | root (UID1) | 5656 | 56 | 24 | 56 | 0 | 0 | 0 | 0 | 0 | 0.00 | 0.00 | 0.00 |
| metabat.3 | k__Bacteria (UID203) | 5449 | 104 | 58 | 71 | 33 | 0 | 0 | 0 | 0 | 46.03 | 0.00 | 0.00 |
| metabat.4 | k__Bacteria (UID203) | 5449 | 104 | 58 | 84 | 20 | 0 | 0 | 0 | 0 | 31.03 | 0.00 | 0.00 |
| metabat.5 | k__Bacteria (UID203) | 5449 | 104 | 58 | 64 | 40 | 0 | 0 | 0 | 0 | 56.90 | 0.00 | 0.00 |
| metabat.6 | o__Pseudomonadales (UID4679) | 87 | 674 | 364 | 16 | 651 | 6 | 1 | 0 | 0 | 97.39 | 1.85 | 11.11 |
| metabat.7 | o__Rhizobiales (UID3447) | 356 | 416 | 249 | 330 | 86 | 0 | 0 | 0 | 0 | 11.85 | 0.00 | 0.00 |
| metabat.8 | c__Gammaproteobacteria (UID4444) | 263 | 506 | 232 | 18 | 478 | 10 | 0 | 0 | 0 | 94.07 | 3.36 | 60.00 |
| metabat.9 | k__Bacteria (UID203) | 5449 | 104 | 58 | 90 | 14 | 0 | 0 | 0 | 0 | 22.41 | 0.00 | 0.00 |
| metabat.10 | c__Gammaproteobacteria (UID4444) | 263 | 507 | 232 | 20 | 476 | 11 | 0 | 0 | 0 | 99.14 | 0.97 | 54.55 |
| metabat.unbinned | k__Bacteria (UID203) | 5449 | 104 | 58 | 25 | 52 | 22 | 4 | 1 | 0 | 66.58 | 22.23 | 27.50 |
</details>
* Et représenter ces résultats sous forme de plots avec `checkm bin_qa_plot`
......@@ -827,7 +826,7 @@ qsub -cwd -V -q formation.q -N checkm -o LOG -e LOG -b y "conda activate checkm-
```
<details>
<summary>Sur le jeu de données réel</summary>
<summary>Résultats attendus</summary>
* [Bar plot of bin quality](html/checkm.png)
</detail>
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Shotgun metagenomics/html/checkm.png
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Shotgun metagenomics/html/checkm.png
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