Question: converting .sra file to fastq file
0
gravatar for josllee
3.6 years ago by
josllee0
United States
josllee0 wrote:

Is there anyway to integrate SRA toolkit into Galaxy? I am trying to analyze raw sra files from GEO but it is a lengthy time to download, convert using the tool kit and then re-upload. Is there an easier way to get .sra files into Galaxy?

tool sra files chip-seq • 6.0k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by josllee0
1
gravatar for Bjoern Gruening
3.6 years ago by
Bjoern Gruening4.8k
Germany
Bjoern Gruening4.8k wrote:

Hi Josilee,

under "Get Data" EBI SRA you can browse the SRA archive and for many datasets you can download fastq files directly into Galaxy. If that is not working for you can install and test the sra toolkit from Matt Shirley

http://toolshed.g2.bx.psu.edu/view/matt-shirley/ncbi_sra_toolkit

Cheers,

Bjoern

 

ADD COMMENTlink written 3.6 years ago by Bjoern Gruening4.8k

Bjoern,

Would you know how to troubleshoot this tool if it only gives a blank page?  Look at this short clip I recorded:

Thanks !

CL

 

ADD REPLYlink written 2.9 years ago by carlos20

No sorry, but have your tried to use the Tool under Get data from your video?

ADD REPLYlink written 2.9 years ago by Bjoern Gruening4.8k

It is a cookie problem - probably as a result of website changes at the EBI side.  If you clear your browser cookies for www.ebi.ac.uk then you will get to see the site - until the next time you follow the galaxy EBI link.  I tried in Chrome and Firefox, same behaviour.

A second issue has cropped up too.  E.g. on https://www.ebi.ac.uk/ena/data/view/SRR031071  .  One must manually select the "NCBI SRA file (galaxy)" field, in order to see it - EVERY TIME one does a search or "Read Files" tab viewing.  So not easy to download a batch of SRA entries this way.

ADD REPLYlink written 2.2 years ago by damiondooley0
0
gravatar for josllee
3.6 years ago by
josllee0
United States
josllee0 wrote:

Hi Bjoern,

Thanks for the advice. I have my own files (not found in the SRA archive) that I need to convert. But thanks for the information for the toolkit!

JL

ADD COMMENTlink written 3.6 years ago by josllee0
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