Ankur Naqib

Hi. Thank you for responding. I did try that. Here is the command I ran- qiime tools import --type "FeatureData[Taxonomy]" --input-format "TSVTaxonomyFormat" --input-path silva_nb.tsv --output-path silva_nb_v3.qza and this is the...

Hi. Formatting it seems like an issue. I can do it but if it becomes part of the code, that will be nice. And that will also allow for easy...

Thank you so much for responding. Yes, we did modify the original run_dada_2023.2.R and made it into the run_dada_2023.2_SingletonTRUE.R (attached in a zip file). We wanted to include singletons detection...

Hi. Yes, I saw that forum too. I wasn't sure which sample was throwing that problem. In the past, I saw that the negative control was throwing that problem so...

Thank you. I will try that. I am starting the pipeline again with the export TMPDIR=\$(pwd) added to the nextflow script. I will let you know as soon as I...

Hi. I went back to using your original pipeline because the customized singletons pipeline was taking too long for me. I just have one issue here. If you see the...

Quick thought. What if I do the allowing singletons approach, and then tag every sample as a different pool of sample, that way every sample will go through the denoising...

Thank you for that. Almost all our reads are over 10k reads. I am going to give it a try. Running 5 samples with and without singletons. And see proportionately,...

Thank you much for all your help and guidance so far. I also wanted to pick your brain about something else. I recently finished a dataset containing 186 files, total...

Yes, within this dataset, I did pool the samples together. I guess I really need to try out running a dataset wherein I tag all the samples as their individual...