MetagenomeILLUMINAIIF5SWPAMPLICONMETAGENOMICRANDOM PRJNA438545SAMN05581709 Īnd from there we can pull out all the run accessions associated with this BioProject we are searching for (along with the same additional information we pulled above), and write it to a file:Įsearch -db sra -query PRJNA438545 | esummary | xtract -pattern DocumentSummary -element > PRJNA438545-info.tsv We can look at it by letting it print some of the the `esummary` to the terminal:Įsearch -db sra -query PRJNA438545 | esummary | head -n 20 This alone, tells us there are 42 hits (in the "Count" field): We still need to get to the run accessions, here we'll start with searching for the bioproject. # Getting info on all runs in the bioproject # Downloading fastq files based on a bioproject (PRJNA.) Then we could download with the run accession (SRR6853380 in this case), the same way we did above with `fasterq-dump`. MetagenomeILLUMINAIIIF1SWPAMPLICONMETAGENOMICRANDOM PRJNA438545SAMN05581714 Īnd we can get some specific info, like here returning the input experiment accession, run accession, and the platform it was sequenced on like so:Įsearch -db sra -query SRX3808505 | esummary | xtract -pattern DocumentSummary -element HiSeq 4000 We can see the xml format of some summary information with this alone:Įsearch -db sra -query SRX3808505 | esummary This toolset is powerful and complicated – more examples can be found on the (). # Starting with "experiment accession" (SRX.) When that's done it will print out something like:Īnd we have two files in our working directory that are each about 1.7GB: Not detailing the programs currently, so see `fasterq-dump -h` for more info on the options available and set here. To download things with `fasterq-dump` as shown here, we want a "run" accession, e.g., SRR6853380:įasterq-dump -split-files -progress SRR6853380 # Example downloading fastq data from NCBI's SRAĬonda create -y -n ncbi-tools -c conda-forge -c bioconda -c defaults sra-tools=2.10.1 entrez-direct=13.9Ĭonda create -y -n pysradb -c conda-forge -c bioconda -c defaults python=3.7 pysradb > **Starter page for a happy belly tutorial on downloading fastq data from SRA.** Title: Examples downloading fastq data from NCBI's SRA
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