sample-metadata file understanding

[turtle]

Hi, I'm trying to use Qiime2R workflow for different sequence data(PRJNA417579) downloaded from SRA database. But the problem I'm having is with the sample-metadata.tsv file, which is used from the tutorial "Moving picture's tutorial".

The main problem is that I wanted to do this qiime2R for my downloaded sequence data. And till now I managed to generate sample-metadata.tsv (209.4 KB) file from metadata.qzv - Google Drive. And tried to run the following r command in Rstudio.

physeq<-qza_to_phyloseq(
  features="dada2_table.qza",
  tree="rooted-tree.qza",
  "taxonomy.qza",
  metadata = "sample-metadata.tsv"
)

But showing this kind of error,

instead of this sample-metadata.tsv file, if I use the same sample-metadata.tsv used in the tutorial from Moving picture and use the file from Moving picture tutorial( taxonomy (1).qza (92.1 KB)rooted-tree (1).qza (64.3 KB)table (1).qza (52.5 KB)) no error is showing.

I also tried to use an edited version of my sample-metadata
sample-metadata_edited.tsv (83.1 KB)
but this also is not helping......

Here is the file I tried to use in above command for PRJNA417579 sequence data.
taxonomy.qza (141.9 KB)
dada2_table.qza (131.6 KB)
rooted-tree.qza (103.7 KB)

[jwdebelius (Justine Debelius)]

Hi @turtle,

This isn't a qiime2R issue, this is a metadata issue. Your metadata should match your samples and should be collected at the time of sampling. (With the exception of long term follow up). Metadata provides context for you samples: collection date, collection time, subject or location, weight, height, chemistry, treatment, temperature... It's an integral part of any experiment, and it needs to match.

The metadata from the moving pictures tutorial won't work for any data but the moving pictures data, and specifically the moving pictures tutorial. I would check what information was deposited in SRA and then I'd go through any accompanying publications or libraries to see if you can find additonal information.

Best,
Justine

[turtle]

Thank you @jwdebelius

Hope you will find some additional information to help me out.

[lizgehret]

Hi @turtle,

Please read @jwdebelius response carefully. You need to obtain appropriate metadata for the sequence data you obtained from the SRA database. Check what information was deposited in SRA and then go through any accompanying publications or libraries to see if you can find additonal information.

Cheers