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population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data

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population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/29 14:57] – [Qiime2 data filtering and feature (OTU) table construction] bnginapopulation-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/29 15:09] (current) – [Qiime2 data filtering and feature (OTU) table construction] bngina
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   *Review the Interactive Quality Plot tab in the //''demux.qzv''// file that was generated by ''qiime demux summarize'' after importing the data to trim of the poor quality bases.    *Review the Interactive Quality Plot tab in the //''demux.qzv''// file that was generated by ''qiime demux summarize'' after importing the data to trim of the poor quality bases. 
   *The expected fragment size after the reads are joined, particularly for the //''--p-trunc-len[f|r]''//.  Refer to the expected fragment length for the primers used to prepare the libraries for sequencing. For example if the expected fragment length for your sequences is 465bp, and lets say the insert size during the sequencing was 300bp. We would want to have a final length of at least 465by or more to have better chances of final sequences of full length for the alignment. Considering that more often than not the forward sequences from illumina sequences have better quality than the reverse sequences. We could use a //''--p-trunc-len-f''// of //''250''// and a //''--p-trunc-len-r''// of //''220''//. to have a final sequence length of //''470bp''//.   *The expected fragment size after the reads are joined, particularly for the //''--p-trunc-len[f|r]''//.  Refer to the expected fragment length for the primers used to prepare the libraries for sequencing. For example if the expected fragment length for your sequences is 465bp, and lets say the insert size during the sequencing was 300bp. We would want to have a final length of at least 465by or more to have better chances of final sequences of full length for the alignment. Considering that more often than not the forward sequences from illumina sequences have better quality than the reverse sequences. We could use a //''--p-trunc-len-f''// of //''250''// and a //''--p-trunc-len-r''// of //''220''//. to have a final sequence length of //''470bp''//.
 +
 +The command would therefore be
 +
 +<code>
 +qiime dada2 denoise-paired \
 + --i-demultiplexed-seqs /home/mydir/qiime2_data/my_raw_data.qza \
 + --p-trim-left-f 0 \
 + --p-trim-left-r 0 \
 + --p-trunc-len-f 250 \
 + --p-trunc-len-r 220\
 + --o-table /home/mydir/qiime2_data/dada2_470_table.qza \
 + --o-representative-sequences /home/mydir/qiime2_data/dada2_470_rep-seqs.qza \
 + --o-denoising-stats /home/mydir/qiime2_data/dada2_470_denoising-stats.qza \
 + --p-n-threads 4
 +
 +#summarise the features table to view it, 
 +        
 +qiime feature-table summarize \
 + --i-table /home/mydir/qiime2_data/dada2_470_table.qza \
 + --o-visualization /home/mydir/qiime2_data/dada2_470_table.qzv
 +
 +
 +#view a summary of the rep sequences
 +
 +qiime feature-table tabulate-seqs \
 + --i-data  /home/mydir/qiime2_data/dada2_470_rep-seqs.qza \
 + --o-visualization  /home/mydir/qiime2_data/dada2_470_rep-seqs.qzv
 +
 +#and also view the denoising statistics
 +qiime metadata tabulate \
 +  --m-input-file /home/mydir/qiime2_data/dada2_470_denoising-stats.qza \
 +  --o-visualization /home/mydir/qiime2_data/dada2_470_denoising-stats.qza
 +</code>
population-diversity/microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data.txt · Last modified: 2020/04/29 15:09 by bngina