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I was trying to download some data from NCBI SRA (SRA059451). There are 27 samples available for SRA059451. But i am unable to understand which samples are 'control' and 'test' samples. Please help me regarding how to differentiate the samples.

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    $\begingroup$ Seems to be cross-posted on Biostars, which is fine but please refer both posts to each other so that answers on one site would be utilized by the other community. $\endgroup$
    – haci
    Mar 19, 2020 at 8:46

1 Answer 1

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You can download the information using this link:

I did it in R:

tab = read.delim("https://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=SRA059451&result=read_run&fields=run_accession,experiment_title,sra_ftp,sample_alias")

head(tab)
  run_accession
1     SRR585697
2     SRR585700
3     SRR585726
4     SRR585727
5     SRR585728
6     SRR585729
                                                                experiment_title
1 Illumina HiSeq 2000 sequencing; Symptomatic atherosclerosis gut metagenome 171
2 Illumina HiSeq 2000 sequencing; Symptomatic atherosclerosis gut metagenome 238
3 Illumina HiSeq 2000 sequencing; Symptomatic atherosclerosis gut metagenome 241
4 Illumina HiSeq 2000 sequencing; Symptomatic atherosclerosis gut metagenome 242
5 Illumina HiSeq 2000 sequencing; Symptomatic atherosclerosis gut metagenome 243
6 Illumina HiSeq 2000 sequencing; Symptomatic atherosclerosis gut metagenome 245
                                      sra_ftp
1 ftp.sra.ebi.ac.uk/vol1/srr/SRR585/SRR585697
2 ftp.sra.ebi.ac.uk/vol1/srr/SRR585/SRR585700
3 ftp.sra.ebi.ac.uk/vol1/srr/SRR585/SRR585726
4 ftp.sra.ebi.ac.uk/vol1/srr/SRR585/SRR585727
5 ftp.sra.ebi.ac.uk/vol1/srr/SRR585/SRR585728
6 ftp.sra.ebi.ac.uk/vol1/srr/SRR585/SRR585729
                                    sample_alias
1     Symptomatic atherosclerosis gut metagenome
2 Symptomatic atherosclerosis gut metagenome 238
3 Symptomatic atherosclerosis gut metagenome 241
4 Symptomatic atherosclerosis gut metagenome 242
5 Symptomatic atherosclerosis gut metagenome 243
6 Symptomatic atherosclerosis gut metagenome 245

Normally the information will be here, but I cannot find what does metagenome 238 etc refers to. No table in the paper that can link sample to phenotype..

Most likely you need to contact the authors. This list might be useful though.

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