I hanve done importing data, but next what should I do?

I have done improting demu data, using the following:

  1. qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path metadata.csv
    –output-path import_results.qza
    –source-format PairedEndFastqManifestPhred33

  2. qiime demux summarize --i-data import_results.qza --o-visualization demux.qzv

  3. qiime dada2 denoise-single
    –p-trim-left 3
    –p-trunc-len 250
    –i-demultiplexed-seqs import_results.qza
    –o-representative-sequences rep-seqs.qza
    –o-table table.qza

  4. qiime quality-filter q-score
    –i-demux import_results.qza
    –o-filtered-sequences demux-filtered.qza
    –o-filter-stats demux-filter-stats.qza

so , netxt what I should do?

I was pareparing to do the next:
qiime feature-table summarize
–i-table table.qza
–o-visualization table.qzv
–m-sample-metadata-file sample-metadata.tsv

but I don’t have sample-metadata.tsv.

Hi @hzh0005,

The next steps really depend on what your scientific questions are, here you can find a few tutorials that might help you decide which commands/analyses to run next.

Now, the sample-metadata.tsv is basically the main information about the samples you are processing. This is something that is normally collected when the samples are collected and without it, it’s impossible to make any sense of the sequences. As the QIIME tutorial puts it: The mapping file is generated by the user. This file contains all of the information about the samples necessary to perform the data analysis. Suggest either generating this file or contacting the people that collected the samples.

Hope this helps.

1 Like

Thanks, I have done as you suggested.

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.