How To Download Sra Files From Ncbi

Download SRA sequences from Entrez search results

Obtain search results

Task: discover RNA-Seq records for lymph node tissue in BALB/c mice in SRA Entrez offsite image

Check To larn how to use Advanced Search Builder please refer to Search in SRA HELP

In the Entrez search bar enter the query: ((("mus musculus"[Organism]) AND BALB/c*) AND "lymph*") AND "rna seq"[Strategy].
To limit your search to just aligned data add together to the to a higher place query AND aligned information"[Backdrop].
Click the checkboxes next to records (experiments) to select data of interest. Leave all checkboxes unchecked to select all records (experiments) from your search.

Obtain run accessions

Run accessions are used to download SRA information. To download a list of Run accessions selected from your Entrez search (Case offsite image ):

Click Send to on the top of the page, check the radiobutton File, select Accretion List.
Salvage this file in the location from which you are running the SRA Toolkit.

SraAccList.txt is formatted like this:

SRR11192680
SRR11192681
SRR11192682
SRR11192683
SRR11192684

Download sequence data files using SRA Toolkit

SRA Run files hold only sequence data and do not contain any metadata (sample data, etc.) linked to the Run.

Exclamation point Delight make sure y'all are running the well-nigh recent release of the toolkit equally older versions may not be uniform with more recently loaded information or the most current network protocols.

Downloading public information

Prefetch is a part of the SRA toolkit. This plan downloads Runs (sequence files in the compressed SRA format) and all boosted data necessary to convert the Run from the SRA format to a more commonly used format. Prefetch tin can be used to correct and finish an incomplete Run download.

Utilize this prefetch command to download the Runs from the previous example in SRA format.

One Run:

$ prefetch SRR000001

A list of Runs:

prefetch --option-file SraAccList.txt

fasterq-dump and sam-dump are besides function of the SRA toolkit and tin can be used to convert the prefetched Runs from compressed SRA format to fastq or sam format. For example:

fasterq-dump --split-files SRR11180057.sra

You lot can also avoid the prefetch step and download and convert the Run in one pace by entering just the Run accession without the .sra extension in your fasterq-dump or sam-dump command:

fasterq-dump --split-files SRR11180057

Downloading Original Submitted Files

SRA has deposited original submitted files into a cloud bucket accessible via the prefetch control if you lot wish to use those instead of dumping standardized data from the archive.

Please refer to Download SRA sequence data using Amazon Web Services (AWS)

An example prefetch command:

prefetch --type fastq SRR11180057

The --blazon command allows you to specify the type of file to download. Yous tin look upwardly the file blazon of the original files in either SRA in BigQuery or the Data Access tab on the Run Browser or use whatever to become all available formats.

Downloading protected data

From the search result folio

SRA Run files practise not contain whatsoever information about the metadata (sample information, etc.) linked to the information themselves.

To download metadata for each Run in your Entrez query click Ship to on the top of the page, check the File radiobutton, and select RunInfo in pull-down menu.

This volition generate a tabular SraRunInfo.csv file with metadata bachelor for each Run.

From Run Selector

A slightly unlike fix of metadata can exist downloaded in a tab-delimited file from Run Selector offsite image .

To download metadata for each Run in your Entrez query:

Click Send to on the top of the folio, check the Run Selector radiobutton, and click the push button Go.
If necessary, refine your results past using various filters provided by the Run Selector'south interface.
Click the RunInfo Table button. This will generate a tabular SraRunTable.txt file with metadata available for each Run.

Download sequence data from the Run Browser

Run Browser offsite image allows for limited download (i run at a time over HTTP) of unaligned and aligned sequences.

Unaligned sequences example

Open the selected run in the Run Browser .
Click the Reads tab.
Find sure reads past applying a Filter or leave the Filter field empty.
Click on the Filtered Download button.
Select bachelor download format and click Download link.

Aligned sequences example

Open the selected run in the Run Browser .
Click the Alignment tab.
Select bachelor download format in pull-down carte and click on Screen or File button to output the run to the screen or into a file.

Download SRA sequence data from the Cloud

Download Trace Archive Data

Trace Archive data now resides in SRA and can be searched in NCBI SRA Entrez like any other SRA data. To limit your search to capillary sequence data, apply the Capillary choice from the Platform section of the results facet list or add "platform capillary"[Properties] to your query. For case, to search for capillary data from the Organism "Mus musculus" use this search:

(Mus muscle[Organism] AND "platform capillary"[Properties])

Once Runs of interest are found, they tin can exist accessed with the SRA toolkit as demonstrated in a higher place. Trace Archive data can be accessed in fasta format by direct query with TI numbers using an SRA spider web service which is described in more than detail on our Admission Trace Data folio.

Contact SRA staff for assistance at sra@ncbi.nlm.nih.gov