file import from other analysis tools

Hi

i am having the following files generated from Parallel-Meta using my metagenome shotgun sequences.

  1. taxa.OTU.Count for multiple samples (single file)
  2. taxa.OTU.abd for multiple samples (single file)
  3. Taxonomical level profile files - taxa.genus.COUNT, taxa.genus.abd for multiple samples
  4. Classification.txt - for individual samples

is it possible to use these files to import and use in QIIME.
Which file to use as OTU file, taxonomy file and how to import them into QIIME
if the classification.txt file has to be used as taxonomy file, then how to merge those individual sample specific classification.txt files into single to import into QIIME

Expecting inputs at the earliest.

Hi @prabugr,

Have you explored the data importing tutorial? There’s a description of how to import feature tables and other types of data.

I would check your documentation, but I think the names should be helpful. You have a taxa.OTU.count - which I would assume is equilivant to a FeatureTable[Frequency] - with per sample counts, a taxa.OTU.abd which I assume is your relative abundance (FeatureTableFeatureTable[RelativeFrequency]). I’m not sure what the taxonomic levels are, I’m going to guess collapsed tables. You may or may not want to import those, but you’d bring them in the same way since they’re feature tables.

Im not so sure about the classification.txt file, if you have a peek inside one, what does it look like? Could you post the first few lines?

Best,
Justine

thanks

the classification.txt file contains the following details

#Database_OTU Count Abundance Taxonomy
25798_117 1 4.72E-06 Bacteria; Patescibacteria; Parcubacteria; Candidatus_Kaiserbacteria; uncultured_bacterium; unidentified; unidentified; otu_25798_117
25131_133 2 9.43E-05 Bacteria; Chloroflexi; Anaerolineae; Ardenticatenales; uncultured; uncultured_bacterium; unidentified; otu_25131_133
2299_122 1 4.72E-05 Bacteria; Planctomycetes; OM190; uncultured_bacterium; unidentified; unidentified; unidentified; otu_2299_122
25798_28 2 9.43E-05 Bacteria; Patescibacteria; Parcubacteria; Candidatus_Kaiserbacteria; uncultured_bacterium; unidentified; unidentified; otu_25798_28
25798_118 6 0.000282971 Bacteria; Patescibacteria; Parcubacteria; Candidatus_Kaiserbacteria; uncultured_bacterium; unidentified; unidentified; otu_25798_118
25131_140 1 4.72E-05 Bacteria; Chloroflexi; Anaerolineae; Ardenticatenales; uncultured; uncultured_bacterium; unidentified; otu_25131_140
2299_118 2 9.43E-05 Bacteria; Planctomycetes; OM190; uncultured_bacterium; unidentified; unidentified; unidentified; otu_2299_118
25798_40 2 9.43E-05 Bacteria; Patescibacteria; Parcubacteria; Candidatus_Kaiserbacteria; uncultured_bacterium; unidentified; unidentified; otu_25798_40
25798_133 2 9.43E-05 Bacteria; Patescibacteria; Parcubacteria; Candidatus_Kaiserbacteria; uncultured_bacterium; unidentified; unidentified; otu_25798_133
25798_128 1 4.72E-05 Bacteria; Patescibacteria; Parcubacteria; Candidatus_Kaiserbacteria; uncultured_bacterium; unidentified; unidentified; otu_25798_128

Hi @prabugr,

I would check and see if you have a similar taxonomic description in one of your taxa.OTU tables, and import that as a taxonomy file. It seems like most of these files are redundant, like your taxa OTU was built out of your classification (for example.) But, if you havrent done it, please also check the parallel meta documentation.

Best,
Justine