Hello, All

I presented my qiime analysis result in my weekly meeting. My senior asked me after the de noising (Dada2 analysis) why sample 6 has very low sequence count and he asked me is it good to take that sample for further analysis.

Before de multiplexing, sample 6 has 85523 sequence count. After de noising, sample 6 has 315 sequence count. I didn't trim or truncate the low quality reads.

De multiplexing step (sequence count of all the sample)

Sample name Sequence count

sample-12 318689

sample-10 316279

sample-9 309068

sample-4 282897

sample-8 268205

sample-7 216594

sample-11 210280

sample-1 173988

sample-3 133036

sample-2 107743

sample-5 90754

sample-6 85523

After dad2 analysis

Sampling depth:

(Zero implies no even sampling.)

Retained 518,292 (100.00%) sequences in 12 (100.00%) samples at the specifed sampling depth.

Number of SamplesSO_8154_S001_ITS1SO_8154_S001_ITS2SO_8154_S006_ITS1SO_8154_S006_ITS2SO_8154_S024_ITS1SO_8154_S024_ITS2SO_8154_S030_ITS1SO_8154_S030_ITS2SO_8154_S034_ITS1SO_8154_S034_ITS2SO_8154_S039_ITS1SO_8154_S039_ITS20.00.10.20.30.40.50.60.70.80.91.0

Sample ID | Sequence Count |
---|---|

sample-9 | 114,019 |

sample-7 | 96,251 |

sample-11 | 82,305 |

sample-10 | 61,008 |

sample-3 | 57,312 |

sample-2 | 36,932 |

sample-5 | 32,659 |

sample-1 | 29,805 |

sample-12 | 2,747 |

sample-4 | 2,476 |

sample-8 | 2,463 |

sample-6 | 315 |

This is the command I ran

qiime dada2 denoise-paired --i-demultiplexed-seqs ITSpaired-end-demux.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 0 --p-trunc-len-r 0 --o-representative-sequences 2ITSrep-seqs-dada2.qza --o-table 2ITStable-dada2.qza --o-denoising-stats 2ITSstats-dada2.qza

Could you please explain me how sequence count value is determined? My opinion about sequence count is number of base pair in sequence. For Instance, Sample 6 has 315 base pair after de noising.

If I am wrong, could anyone please explain about that sequence count?

One more query is what is the minimum OTU sequence length to consider as valid OTU sequence

?

Thanking you in advance. Looking forward to your reply.