溫馨提示×
您好，登錄后才能下訂單哦！
點擊 登錄注冊 即表示同意《億速云用戶服務條款》
您好，登錄后才能下訂單哦！
本篇內容主要講解“怎么用qiime2分類器建立SILVA數據庫”，感興趣的朋友不妨來看看。本文介紹的方法操作簡單快捷，實用性強。下面就讓小編來帶大家學習“怎么用qiime2分類器建立SILVA數據庫”吧!
利用工具建立數據庫 rescript
qiime rescript get-silva-data \--p-version '138' \ --p-target 'SSURef_NR99' \ --p-include-species-labels \ --o-silva-sequences silva-138-ssu-nr99-seqs.qza \ --o-silva-taxonomy silva-138-ssu-nr99-tax.qza
這個代碼自動獲取 99相似性的序列和分類信息，由于網絡原因一般運行報錯
wget -c https://data.qiime2.org/2020.8/common/silva-138-99-seqs.qza wget -c https://data.qiime2.org/2020.8/common/silva-138-99-tax.qza ln -s silva-138-99-tax.qza silva-138-ssu-nr99-tax.qza ln -s silva-138-99-seqs.qza silva-138-ssu-nr99-seqs.qza
#remove sequences that contain 5 or more ambiguous bases (IUPAC compliant ambiguity bases) and any homopolymers that are 8 or more bases in length qiime rescript cull-seqs \ --i-sequences silva-138-ssu-nr99-seqs.qza \ --o-clean-sequences silva-138-ssu-nr99-seqs-cleaned.qza #長度過濾 qiime rescript filter-seqs-length-by-taxon \ --i-sequences silva-138-ssu-nr99-seqs-cleaned.qza \ --i-taxonomy silva-138-ssu-nr99-tax.qza \ --p-labels Archaea Bacteria Eukaryota \ --p-min-lens 900 1200 1400 \ --o-filtered-seqs silva-138-ssu-nr99-seqs-filt.qza \ --o-discarded-seqs silva-138-ssu-nr99-seqs-discard.qza #重復序列合并 qiime rescript dereplicate \ --i-sequences silva-138-ssu-nr99-seqs-filt.qza \ --i-taxa silva-138-ssu-nr99-tax.qza \ --p-rank-handles 'silva' \ --p-mode 'uniq' \ --o-dereplicated-sequences silva-138-ssu-nr99-seqs-derep-uniq.qza \ --o-dereplicated-taxa silva-138-ssu-nr99-tax-derep-uniq.qza #全長分類器構建 qiime feature-classifier fit-classifier-naive-bayes \ --i-reference-reads silva-138-ssu-nr99-seqs-derep-uniq.qza \ --i-reference-taxonomy silva-138-ssu-nr99-tax-derep-uniq.qza \ --o-classifier silva-138-ssu-nr99-classifier.qza ##特異引物分類器構建1 #截取序列 qiime feature-classifier extract-reads \ --i-sequences silva-138-ssu-nr99-seqs-derep-uniq.qza \ --p-f-primer GTGYCAGCMGCCGCGGTAA \ --p-r-primer GGACTACNVGGGTWTCTAAT \ --p-n-jobs 2 \ --p-read-orientation 'forward' \ --o-reads silva-138-ssu-nr99-seqs-515f-806r.qza #合并重復 qiime rescript dereplicate \ --i-sequences silva-138-ssu-nr99-seqs-515f-806r.qza \ --i-taxa silva-138-ssu-nr99-tax-derep-uniq.qza \ --p-rank-handles 'silva' \ --p-mode 'uniq' \ --o-dereplicated-sequences silva-138-ssu-nr99-seqs-515f-806r-uniq.qza \ --o-dereplicated-taxa silva-138-ssu-nr99-tax-515f-806r-derep-uniq.qza #構建分類器 qiime feature-classifier fit-classifier-naive-bayes \ --i-reference-reads silva-138-ssu-nr99-seqs-515f-806r-uniq.qza \ --i-reference-taxonomy silva-138-ssu-nr99-tax-515f-806r-derep-uniq.qza \ --o-classifier silva-138-ssu-nr99-515f-806r-classifier.qza ##特異引物分類器構建2 # 338F (5′-ACTCCTACGGGAGGCAGCAG-3′) and. 806R (5′-GGACTACHVGGGTWTCTAAT-3′) #截取序列 qiime feature-classifier extract-reads \ --i-sequences silva-138-ssu-nr99-seqs-derep-uniq.qza \ --p-f-primer ACTCCTACGGGAGGCAGCAG \ --p-r-primer GGACTACHVGGGTWTCTAAT \ --p-n-jobs 2 \ --p-read-orientation 'forward' \ --o-reads silva-138-ssu-nr99-seqs-338f-806r.qza #合并重復 qiime rescript dereplicate \ --i-sequences silva-138-ssu-nr99-seqs-338f-806r.qza \ --i-taxa silva-138-ssu-nr99-tax-derep-uniq.qza \ --p-rank-handles 'silva' \ --p-mode 'uniq' \ --o-dereplicated-sequences silva-138-ssu-nr99-seqs-338f-806r-uniq.qza \ --o-dereplicated-taxa silva-138-ssu-nr99-tax-338f-806r-derep-uniq.qza #構建分類器 qiime feature-classifier fit-classifier-naive-bayes \ --i-reference-reads silva-138-ssu-nr99-seqs-338f-806r-uniq.qza \ --i-reference-taxonomy silva-138-ssu-nr99-tax-338f-806r-derep-uniq.qza \ --o-classifier silva-138-ssu-nr99-338f-806r-classifier.qza
注意：qiime2建立分類數據庫很消耗內存，至少50G以上
到此，相信大家對“怎么用qiime2分類器建立SILVA數據庫”有了更深的了解，不妨來實際操作一番吧！這里是億速云網站，更多相關內容可以進入相關頻道進行查詢，關注我們，繼續學習！
免責聲明：本站發布的內容（圖片、視頻和文字）以原創、轉載和分享為主，文章觀點不代表本網站立場，如果涉及侵權請聯系站長郵箱：is@yisu.com進行舉報，并提供相關證據，一經查實，將立刻刪除涉嫌侵權內容。
