Dear all, I am analysing fungi data obtained from a capillery sequencer. I have converted the fasta file to fastq files using seqtk. After loading them into QIIME2 using the type paired end sequencing and the result I am getting from the qzv file is only 1 sequence per sample. So I separated the f…

When I was speaking of the quality scores, I was referring to using DADA2. As you mentioned you were going to use... Denoising tools, like DADA2 require FASTQ files. [image] sree: If there is anyway I can simply import and use the fasta files and do the alignment and taxonomy mapping and furth…

Hello @sree , Which command did you use to import the sequences? How many sequences do you expect to have per sample? Do you have one fastq file per sample? Does capillary sequencing produce two read directions?

Dear @colinvwood I created manifest file to import the data. Per sample using grep command I am getting around 400 to 600 bp. No I have forward and reverse Fasta file not Fastq file. So I converted all the forward and reverse Fasta file to Fastq files using Seqtk. Yes, the data I have is generated …

Hello @sree , I meant how many sequences per sample, not base pairs per sequence. Would you mind attaching one of the fastq files that you have, if it's not too large? If it is too large, could you take the first 100 records or so and attach those?

PCR_14_sample1R1.txt (325 Bytes) PCR_14_sample1R2.txt (574 Bytes) PCR_14_ITS_1_F02.fastq (604 Bytes) PCR_14_ITS_4_F02.fastq (1.1 KB) I am unable to upload the fasta file so attached it as text. I have also attached the converted fastq files

Hi @sree , Looking at the fastq files you uploaded it looks like these files only have one sequence per sample. If this is not what you are expecting, I think you will have to talk to the individuals that generated the data.

Dear @cherman2 This is actually forward and reverse sample of PCR 14 and this is generated from capillary sequencer. I am stuck with the analysis because most of the samples are going after creating the table file. So now I am individually analysing the samples and planning to merge the rep.seqs a…

Hello @sree , I'm unsure what you mean by "the samples are going after creating the table file". I think that the nature of your data is possibly such that it doesn't make much sense to analyze with qiime2, given that you only have one sequence per sample and thus will have only one feature per samp…

Dear @colinvwood I understand that. Samples I meant to say sequences. Since Per sample I have one sequence, after quality control many samples are going and out of 19 samples I am left with only one or two files to go for taxonomy profiling. If Qiime2 is not a good option for my analysis could you …

Hello @sree , If Qiime2 is not a good option for my analysis could you please let me know what is a better way. It depends on what your goal is. Diversity analyses are going to be difficult and not very meaningful with such a small number of features.

[image] sree: If Qiime2 is not a good option for my analysis could you please let me know what is a better way. Shall QIIME2 developing with the function for one sequence testing or annotiation in the future? @colinvwood I think this post author need a one sequence service from qiime2-platfor…

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