Friday, January 24, 2014

How to download Fastq files from SRA archive

If you want to download sequence reads from the SRA archive you can do this in their .sra format which then you need to transform to fastq using the SRA toolkit.

However you can also download directly fastq files from the SRA archive:

Go to your run and copy the Experiment number, e.g. SRX157609

Go to Download
FASTA/FASTQ
Enter Experiment number
Select Fastq
Download

How to make Fastq files from SRA to be recognized by Galaxy

If you downloaded Fastq files from SRA database and if you uploaded these files to Galaxy and Galaxy is not able to recognize them as fastq files for Bowtie or BWA mapping, you need to change the attributes of the fastq files.

Go to Edit attributes.
Datatype
Change from fastq to fastqsanger
Save

After this your files will be present at the dropdown menu when zou select Bowtie or BWA