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PacBio ITS workflow - some questions
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4
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106
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September 9, 2026
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Very low percentage of merged reads in DADA2 with 16S V4, 2×150 bp paired-end sequencing
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3
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53
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August 28, 2026
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Why are my reads filtered out (98%) when quality seems okay?
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6
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105
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August 20, 2026
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Why truncate with dada2 when ITSxpress is an option?
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16
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257
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August 17, 2026
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Request: DADA2 denoise-ccs without --p-front parameter
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2
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60
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August 4, 2026
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Is my truncation parameter exploration sufficient, and is my interpretation correct?
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1
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56
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July 28, 2026
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Losing reads at DADA2 Merge step 30% of my samples lost over 50% - I have tried multiple steps to fix- please help
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1
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49
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July 21, 2026
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Can DADA2 be used with nearly uniform Q38 quality scores?
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2
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60
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July 21, 2026
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Sequencing platform fully confounded with study period: MiSeq vs NextSeq 2000 (16S rRNA V3-V4)
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3
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89
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July 7, 2026
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QIIME 2 processing of MiSeq i100 data with constant quality scores
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3
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146
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June 8, 2026
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Running DADA2 on pre-processed data
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7
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156
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June 3, 2026
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Query about false read merging or no read merging
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1
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43
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May 26, 2026
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Merging NGS with TGS?
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3
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70
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May 20, 2026
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Under the hood of the "Moving Pictures" tutorial
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0
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182
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May 13, 2026
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sequence alignment
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5
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79
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May 11, 2026
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An error was encountered while running DADA2 in R (return code 1), inspect stdout and stderr to learn more
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10
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140
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May 8, 2026
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Help - DADA2 microbiome analysis
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3
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78
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May 4, 2026
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Qiime version and singletons
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3
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89
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April 27, 2026
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High number of unique sequences in PacBio full-length 16S CCS data with DADA2
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2
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139
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April 24, 2026
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Low overlap due to poor reverse read quality in 2×300 bp V3–V4 amplicon sequencing (DADA2)
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1
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87
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April 13, 2026
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High but variable sequence loss (32-68%) during DADA2 filtering with V3-V4 amplicons (MiSeq 600 cycles)
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2
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115
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April 9, 2026
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Inadequate overlap for V3-V4 (paired-end) due to quality drop
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5
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130
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March 9, 2026
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Integrating V3-V4 and V4 16S datasets for large-scale meta-analysis: Is Greengenes2 the optimal choice for cross-region alignment?
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1
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173
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March 6, 2026
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Too many elements for DADA2 - denoise in batches?
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6
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149
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March 4, 2026
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Analysis with DADA2... Merge Read Length
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1
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67
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March 4, 2026
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denoise failure
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5
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87
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February 24, 2026
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Huge difference of DADA2 output with and without removing primers
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4
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128
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January 27, 2026
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Advice in best practice for handling multiple sequencing runs and subset analyses in QIIME 2 (DADA2)
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2
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132
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January 16, 2026
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pair ended demultiplexed qza file causing strange error.
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1
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65
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December 28, 2025
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High read loss due to artifacts and chimera after denoising 16S V3-V4 paired-end reads
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1
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89
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December 17, 2025
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