{"id":3,"date":"2024-04-04T08:51:35","date_gmt":"2024-04-04T05:51:35","guid":{"rendered":"https:\/\/sisu.ut.ee\/eukaryome\/how\/"},"modified":"2024-10-25T16:28:27","modified_gmt":"2024-10-25T13:28:27","slug":"how","status":"publish","type":"page","link":"https:\/\/sisu.ut.ee\/eukaryome\/how\/","title":{"rendered":"Tips on integration"},"content":{"rendered":"

1. QIIME 2 Integration with EUKARYOME<\/strong><\/span><\/p>\n

1.1. Importing EUKARYOME into QIIME 2<\/span><\/strong><\/p>\n

Initially, you should change the format to the \u201c.qza\u201d format and import the files into QIIME 2:<\/p>\n

Importing the taxonomy file:<\/strong><\/span><\/p>\n

\nqiime tools import --type 'FeatureData[Taxonomy]' --input-path QIIME2_EUK_SSU_v1.8.tsv --output-path eukaryome_tax.qza\n<\/code><\/pre>\n
Importing the sequence file:<\/strong><\/span><\/p>\n
\nqiime tools import --input-path QIIME2_EUK_SSU_v1.8.fasta --output-path eukaryome_seq.qza --type 'FeatureData[Sequence]'\n<\/code><\/pre>\n
1.2. Taxonomic analysis<\/strong><\/span><\/p>\n
With the database imported, you can now perform taxonomic analysis. The taxonomic classification can be performed with different plugins; see the basic scripts below:<\/p>\n
Feature Classifier Plugin:<\/strong><\/span><\/p>\n
\nqiime feature-classifier fit-classifier-naive-bayes --i-reference-reads eukaryome_seq.qza --i-reference-taxonomy eukaryome_tax.qza --o-classifier classifier.qza\n<\/code><\/pre>\n
Then, you can assign taxonomy to your sequences using the trained classifier:<\/p>\n
\nqiime feature-classifier classify-sklearn --i-classifier classifier.qza --i-reads your_sequences.qza --o-classification taxonomy.qza\n<\/code><\/pre>\n
Blast+ plugin:<\/strong><\/p>\n
\nqiime feature-classifier classify-consensus-blast --i-query your_sequences.qza --i-reference-reads eukaryome_seq.qza --i-reference-taxonomy eukaryome_tax.qza --p-perc-identity 0.97 --o-classification taxonomy.qza\n<\/code><\/pre>\n
Please note that these are basic scripts and may need to be adjusted based on your specific needs and the parameters of your data.<\/strong><\/em><\/p>\n
2. mothur Integration with EUKARYOME<\/strong><\/span><\/p>\n
Here are the following basic scripts to use with different methods in mothur:<\/p>\n
\n# Wang method (default)\nmothur \"#classify.seqs(fasta=your_sequences.fasta, reference=mothur_SSU_v1.8.fasta, taxonomy=mothur_SSU_v1.8.tax, method=wang, cutoff=80)\"\n\n# k-nearest neighbor consensus\nmothur \"#classify.seqs(fasta=your_sequences.fasta, reference=mothur_SSU_v1.8.fasta, taxonomy=mothur_SSU_v1.8.tax, method=knn, cutoff=80)\"\n\n# Zap\nmothur \"#classify.seqs(fasta=your_sequences.fasta, reference=mothur_SSU_v1.8.fasta, taxonomy=mothur_SSU_v1.8.tax, method=zap, cutoff=80)\"\n<\/code><\/pre>\n
Please note that these are basic scripts and may need to be adjusted based on your specific needs and the parameters of your data<\/strong><\/em>.<\/p>\n
3. SINTAX Integration with EUKARYOME<\/strong><\/span><\/p>\n
To perform taxonomic analysis using SINTAX and the EUKARYOME database, use the following commands:<\/p>\n
#converting to udb format:<\/code><\/pre>\n
vsearch --makeudb_usearch SINTAX_SSU_v1.8.fasta --output SINTAX_SSU.udb \n\n#assign taxonomy:<\/code><\/pre>\n
vsearch --sintax your_sequences.fasta -db SINTAX_SSU.udb -tabbedout sintax_results.txt -sintax_cutoff 0.8\n<\/code><\/pre>\n
Please note that these are basic scripts and may need to be adjusted based on your specific needs and the parameters of your data<\/strong><\/em>.<\/p>\n
4. BLAST<\/strong><\/span><\/p>\n
First, you must format your fasta file into a BLAST database using the makeblastdb command. This command will create a nucleotide BLAST database from your fasta file:<\/p>\n
\nmakeblastdb -in General_SSU_v1.8.fasta -dbtype nucl -out EUK_SSU.DB\n<\/code><\/pre>\n
Then you can use blastn with your input sequences and the BLAST database:<\/p>\n
\nblastn -query your_sequences.fasta -db EUK_SSU.DB -out results.out\n<\/code><\/pre>\n
Please refer to the BLAST+ manual or other relevant resources for more advanced usage.<\/strong><\/em><\/p>\n
5. DADA2<\/strong><\/span><\/p>\n
To perform taxonomic analysis using the DADA2 classifier and the EUKARYOME database, use the following commands:<\/p>\n
<\/code>library(dada2)
\nasv <- \"input.fasta\"
\ndatabase <- \"DADA2_EUK_ITS_v1.9.fasta\"
\ntaxa_output_file <- \"taxonomy_result.csv\"
\ntaxonomy <- assignTaxonomy(asv,database, multithread =8)
\n<\/code>write.csv(taxonomy, file = taxa_output_file)<\/code><\/p>\n
Please refer to the DADA2 manual or other relevant resources for more advanced usage.<\/strong><\/em><\/p>\n","protected":false},"excerpt":{"rendered":"
1. QIIME 2 Integration with EUKARYOME 1.1. Importing EUKARYOME into QIIME 2 Initially, you should change the format to the \u201c.qza\u201d format and import the files into QIIME 2: Importing the taxonomy file: qiime tools import –type ‘FeatureData[Taxonomy]’ –input-path QIIME2_EUK_SSU_v1.8.tsv …<\/p>\n","protected":false},"author":163,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":""},"class_list":["post-3","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/pages\/3","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/users\/163"}],"replies":[{"embeddable":true,"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/comments?post=3"}],"version-history":[{"count":22,"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/pages\/3\/revisions"}],"predecessor-version":[{"id":498,"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/pages\/3\/revisions\/498"}],"wp:attachment":[{"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/media?parent=3"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}