# 激活工作环境source activate qiime2-2017.8# 建立工作目录mkdir -p qiime2-importing-tutorialcd qiime2-importing-tutorial
导入带质量值的测序数据
地球微生物组标准混样单端数据 “EMP protocol” multiplexed single-end fastq
此类数据标准包括两个文件，扩展名均为fastq.gz，一个是barcode文件，一个是样品混样测序文件。
# 建样品目录mkdir -p emp-single-end-sequences# 下载 barcode文件wget -O emp-single-end-sequences/barcodes.fastq.gz https://data.qiime2.org/2017.8/tutorials/moving-pictures/emp-single-end-sequences/barcodes.fastq.gz# 下载序列文件wget -O emp-single-end-sequences/sequences.fastq.gz https://data.qiime2.org/2017.8/tutorials/moving-pictures/emp-single-end-sequences/sequences.fastq.gz# 导入QIIME2格式qiime tools import \ --type EMPSingleEndSequences \ --input-path emp-single-end-sequences \ --output-path emp-single-end-sequences.qza
地球微生物组标准混样双端数据 “EMP protocol” multiplexed paired-end fastq
此类数据标准包括三个文件，扩展名均为fastq.gz，一个是barcode文件，两个是样品混样测序文件。
# 建样品目录mkdir -p emp-paired-end-sequences# 下载序列正向和反向文件wget -O emp-paired-end-sequences/forward.fastq.gz https://data.qiime2.org/2017.8/tutorials/atacama-soils/1p/forward.fastq.gzwget -O "emp-paired-end-sequences/reverse.fastq.gz https://data.qiime2.org/2017.8/tutorials/atacama-soils/1p/reverse.fastq.gz # 下载barcode文件wget -O emp-paired-end-sequences/barcodes.fastq.gz https://data.qiime2.org/2017.8/tutorials/atacama-soils/1p/barcodes.fastq.gz # 导入QIIME2格式qiime tools import \ --type EMPPairedEndSequences \ --input-path emp-paired-end-sequences \ --output-path emp-paired-end-sequences.qza
样品文件清单格式 “Fastq manifest” formats
# 下载fastq压缩包zip文件，其中的样品文件和清单文件mainfestwget -O se-33.zip https://data.qiime2.org/2017.8/tutorials/importing/se-33.zipwget -O se-33-manifest https://data.qiime2.org/2017.8/tutorials/importing/se-33-manifestwget -O pe-64.zip https://data.qiime2.org/2017.8/tutorials/importing/pe-64.zipwget -O pe-64-manifest https://data.qiime2.org/2017.8/tutorials/importing/pe-64-manifest# 解压fastq样品文件unzip -q se-33.zipunzip -q pe-64.zip
样品清单是包括样品名、文件位置、文件方向三列的csv文件，以pe-64-manifest为例，内容如下：
# 样品名、文件位置、文件sample-id,absolute-filepath,directionsample1,$PWD/pe-64/s1-phred64-r1.fastq.gz,forwardsample1,$PWD/pe-64/s1-phred64-r2.fastq.gz,reversesample2,$PWD/pe-64/s2-phred64-r1.fastq.gz,forwardsample2,$PWD/pe-64/s2-phred64-r2.fastq.gz,reverse
导入质量值不同编码的两类文件Phred33/64 (一般 Phred33比较常见，只有非常老的数据才有Phred64格式)
# 导入Phred33格式测序结果qiime tools import \ --type 'SampleData[SequencesWithQuality]' \ --input-path se-33-manifest \ --output-path single-end-demux.qza \ --source-format SingleEndFastqManifestPhred33# 导入Phred64格式测序结果qiime tools import \ --type 'SampleData[PairedEndSequencesWithQuality]' \ --input-path pe-64-manifest \ --output-path paired-end-demux.qza \ --source-format PairedEndFastqManifestPhred64
导入OTU表Biom文件
BIOM v1.0.0
# 下载数据并导入为QIIME2的qza格式wget -O feature-table-v100.biom https://data.qiime2.org/2017.8/tutorials/importing/feature-table-v100.biomqiime tools import \ --input-path feature-table-v100.biom \ --type 'FeatureTable[Frequency]' \ --source-format BIOMV100Format \ --output-path feature-table-1.qza
BIOM v2.1.0
wget -O feature-table-v210.biom https://data.qiime2.org/2017.7/tutorials/importing/feature-table-v210.biomqiime tools import \ --input-path feature-table-v210.biom \ --type 'FeatureTable[Frequency]' \ --source-format BIOMV210Format \ --output-path feature-table-2.qza
代表性序列 Per-feature unaligned sequence data
wget -O sequences.fna https://data.qiime2.org/2017.8/tutorials/importing/sequences.fnaqiime tools import \ --input-path sequences.fna \ --output-path sequences.qza \ --type 'FeatureData[Sequence]'
多序列比对后的代表性序列导入(多序列比对后的序列中包括减号，表示比对的gap) Per-feature unaligned sequence data
wget -O aligned-sequences.fna https://data.qiime2.org/2017.8/tutorials/importing/aligned-sequences.fnaqiime tools import \ --input-path aligned-sequences.fna \ --output-path aligned-sequences.qza \ --type 'FeatureData[AlignedSequence]'
无根进化树导入 Phylogenetic trees (unrooted)
wget -O unrooted-tree.tre https://data.qiime2.org/2017.8/tutorials/importing/unrooted-tree.treqiime tools import \ --input-path unrooted-tree.tre \ --output-path unrooted-tree.qza \ --type 'Phylogeny[Unrooted]'