Convert SRA format to fastq

Sep 09, 2011

NCBI GEO uses SRA (Sequence Read Archive) format to store sequencing files. e.g.

SRA format needs to be converted into fastq to be used as input to Bowtie, Tophat etc. Here is how:

Download the SRA toolkit from http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software

If you are using 64-bit linux, try the CentOS Linux 64 bit architecture first. It is so much pain to compile from source.
Decompress the downloaded file, and copy the fastq-dump file to system path.
Convert SRA to fastq
```
 fastq-dump SRA_archive_file.sra
```
which will create a fastq file with the same name as the SRA archive file.

References:

azalea says