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Download and Extract Reads in BAM (version 3.1.0+galaxy1)
Must start with SRR, DRR or ERR, e.g. SRR925743, ERR343809
In vast majority of cases you want to download data in bam format. It is more compact and is accepted by all downstream tools.
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What it does?

This tool extracts data (in BAM format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the sam-dump utility of the SRA Toolkit and returns a collection of NGS data containing one file for each accession number provided.

How to use it?

There are three ways in which you can download data:

  1. Plain text input of accession number(s)
  2. Providing a list of accessions from file
  3. Extracting data from an already uploaded SRA dataset

Below we discuss each in detail.

Plain text input of accession number(s)

When you type an accession number (e.g., SRR1582967) into Accession box and click Execute the tool will fetch the data for you. You can also provide a list of multiple accession numbers (e.g. SRR3141592, SRR271828, SRR112358).

Providing a list of accessions from file

A more realistic scenario is when you want to upload a number of datasets at once. To do this you need a list of accession, where there is only one accession per line (see below for information on how to generate such a file). Once you have this file:

  1. Upload it into your history using Galaxy's upload tool
  2. Once the list of accessions is uploaded choose List of SRA accessions, one per line from select input type dropdown
  3. Choose uploaded file within the sra accession list field
  4. Click Execute

Extract data from an already uploaded SRA dataset

If an SRA dataset is already present in the history, the sequencing data can be extracted in a human-readable data format (fastq, sam, bam) by setting select input type drop-down to SRA archive in current history.

How to generate accession lists

  1. Go to SRA Run Selector by clicking this link
  2. Find the study you are interested in by typing a search term within the Search box. This can be a word (e.g., mitochondria) or an accession you have gotten from a paper (e.g., SRR1582967).
  3. Once you click on the study of interest you will see the number of datasets in this study within the Related SRA data box
  4. Click on the Runs number
  5. On the page that would open you will see Accession List button
  6. Clicking of this button will produce a file that you will need to upload into Galaxy and use as the input to this tool.

For credits, information, support and bug reports, please refer ato https://github.com/galaxyproject/tools-iuc.