Open rx32940 opened 4 years ago
The following code should:
/scratch/rx32940/CLARK/CLARKSCV1.2.6.1/result_genus
/scratch/rx32940/CLARK/output/genus_custom_spaced
the spaced database is building on sapelo2 with both prebuilt Clark database as well as the custom database.
Results for prebuilt regular database:
/scratch/rx32940/CLARK/output/prebuilt/genus(phylum/species)/regular
Results for prebuilt spaced database:
/scratch/rx32940/CLARK/output/prebuilt/genus(phylum/species)/spaced
Results for custom regular database:
/scratch/rx32940/CLARK/output/custom/genus(phylum/species)/regular
Results for custom spaced database:
/scratch/rx32940/CLARK/output/custom/genus(phylum/species)/spaced
- [x] Phylum level analysis (regular and spaced with custom database)
- [x] r visualization barplot fro phylum level analysis
- [ ] genus level analysis (regular and spaced with custom database)
- [ ] top 10 most abundant genus
- [ ] species level analysis (regular and spaced with custom database)
Clark-s custom database results
/Users/rx32940/Dropbox/5.Rachel-projects/Metagenomic_Analysis/Clark-s/phylum/classifiedOnly_Count_clarks_phylum_custom.csv
/Users/rx32940/Dropbox/5.Rachel-projects/Metagenomic_Analysis/Clark/phylum/results/classifiedOnly_percentage_clark_phylum_custom.csv
[x] Clark-s prebuilt database (26)
/Users/rx32940/Dropbox/5.Rachel-projects/Metagenomic_Analysis/Clark-s/phylum/prebuilt/classifiedOnly_Count_clark_phylum_custom.csv
[x] Clark prebuilt database (41)
/Users/rx32940/Dropbox/5.Rachel-projects/Metagenomic_Analysis/Clark/phylum/prebuilt/classifiedOnly_count_clark_phylum_prebuilt.csv
[x] kraken2 custom database (31) r visualization of the kraken2/bracken phylum level classification with custom database
/Users/rx32940/Dropbox/5.Rachel-projects/Metagenomic_Analysis/Kraken2-standard/custom/phylum/bracken_%_custom_phylum.csv
[x] kraken2 standard database kraken2 standard database results
thus all phylum classified by Clark-s with custom database were plotted here.
Sample ID | Classified (%) | Unclassified (%) |
---|---|---|
R22.K | 82.4363 | 17.5637 |
R22.L | 28.7164 | 71.2836 |
R22.S | 73.2934 | 26.7066 |
R26.K | 77.8431 | 22.1569 |
R26.L | 48.262 | 51.738 |
R26.S | 72.1112 | 27.8888 |
R27.K | 72.597 | 27.403 |
R27.L | 31.2137 | 68.7863 |
R27.S | 71.7787 | 28.2213 |
R28.K | 90.76 | 9.24 |
R28.L | 88.6129 | 11.3871 |
R28.S | 89.0807 | 10.9193 |
dir for the table above:
/Users/rx32940/Dropbox/5.Rachel-projects/Metagenomic_Analysis/Clark-s/phylum/clarks_custom_phylum_%_classified.xlsx
dir with the exact number of classified reads and percentage of the reads excluding the UNKNOWN reads:
/Users/rx32940/Dropbox/5.Rachel-projects/Metagenomic_Analysis/Clark-s/phylum/classifiedOnly_Count_clarks_phylum_custom.csv
/Users/rx32940/Dropbox/5.Rachel-projects/Metagenomic_Analysis/Clark-s/phylum/classifiedOnly_percentage_clarks_phylum_custom.csv
classification with a prebuilt database shows a very low classification level, thus will not be considered.
Sample ID | Classified (%) | Unclassified (%) |
---|---|---|
R22.K | 10.4762 | 89.5238 |
R22.L | 6.2897 | 93.7103 |
R22.S | 12.3613 | 87.6387 |
R26.K | 12.786 | 87.214 |
R26.L | 7.2184 | 92.7816 |
R26.S | 8.9735 | 91.0265 |
R27.K | 15.6412 | 84.3588 |
R27.L | 6.2805 | 93.7195 |
R27.S | 8.3282 | 91.6718 |
R28.K | 6.7079 | 93.2921 |
R28.L | 5.1649 | 94.8351 |
R28.S | 4.5048 | 95.4952 |
From the percent of classified reads file, I concluded that:
dir to the classified percentage file:
/Users/rx32940/Dropbox/5.Rachel-projects/Metagenomic_Analysis/Clark-s/phylum/clarks_custom_phylum_%_classified.xlsx
Sample ID | Classified (%) | Unclassified (%) |
---|---|---|
R22.K | 76.8498 | 23.1502 |
R22.L | 25.789 | 74.211 |
R22.S | 66.2754 | 33.7246 |
R26.K | 73.5044 | 26.4956 |
R26.L | 42.8965 | 57.1035 |
R26.S | 64.2384 | 35.7616 |
R27.K | 70.1686 | 29.8314 |
R27.L | 27.828 | 72.172 |
R27.S | 64.6651 | 35.3349 |
R28.K | 80.2579 | 19.7421 |
R28.L | 78.6874 | 21.3126 |
R28.S | 79.2095 | 20.7905 |
dir for the results:
/Users/rx32940/Dropbox/5.Rachel-projects/Metagenomic_Analysis/Clark-s/genus/results
/Users/rx32940/Dropbox/5.Rachel-projects/Metagenomic_Analysis/Clark/genus/results
https://github.com/rx32940/Lepto-Metagenomics/issues/3#issuecomment-547548115