Sra Format Usage - How To

Question

[Daniel]

Could somebody please explain in easy terms how to use SRA format files from NCBI Sequence Read Archive? The files are large, so I use the Aspera plugin to download them. The documentation on NCBI (http://www.ncbi.nlm.nih.gov/books/NBK47540/#SRA_Download_Guid_B.3_Installing_the_Too) is hard to follow. I need to convert the files to fasta or fastq or sff. Thanks for any help.

Answer 1

[Sukhi Singh]

You need SRA-Toolkit to filter what you want from the SRA archive (a mixture of raw files and other metadata.) For instance, I have this ChIP-Seq data in the .sra format here. I will jus tuse wget to pull it and the extract the fastq files from it using the tool called fastq-dump included in the SRA-Toolkit.

Usage:
  sratoolkit/fastq-dump [options] [ -A ] <accession>
  sratoolkit/fastq-dump [options] <path [path...]>

Check the complete manual of fastq-dump

Grab you copy of SRA-Toolkit, depending on your software architecture.

Cheers

[Neilfws]

I'm afraid there is no simple, non-technical answer to your question. You need the SRA Toolkit and you need to understand how to install and use it, which means reading the documentation and experimenting until you understand enough to make it work. I wrote a blog post which might help: http://nsaunders.wordpress.com/2011/12/22/sequencing-for-relics-from-the-sanger-era-part-1-getting-the-raw-data/

[Neilfws]

These additional questions were posted as an answer which has been removed:

1. So I need to have the file downloaded as .sra.
2. I need to download the toolkit and use the fastq-dump.2.1.18 bin (binary?) program. I guess I can run it on Mac from terminal?
3. Which command line should I use? Is this in any way dependent on the sequencing platform that was used to generate the sra data (eg Ilimuina, 454, etc)?

Answer 2

[hithesh]

To Convert SRA to Fastq

use this command

open SRA toolkit kit path

open bin folder

fastq-dump.exe pathfile\filename outputfilename

Answer 3

[gaughey]

I know this is an old question, but I've just spent the afternoon wrestling with SRA-Toolkit as suggested by other answers - my computer seems not to like it -or I'm too stupid to make it work. So I thought I should point out that there is a way to solve this problem using galaxy for computer illiterates like me! Go to usegalaxy.org. Under the tab "NCBI SRA Tools" there are some options for extracting reads in Bam or fastq format - all you have to do is input the accession number!