Question: How to convert SRA Files to FASTAQ files in a 32 BIt windows computer ( beginner here)
0
gravatar for rahulraghavantv
2.9 years ago by
rahulraghavantv0 wrote:

How to convert SRA Files to FASTAQ files in a 32 BIt windows computer ( beginner here)

fastq sra galaxy • 2.1k views
ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by rahulraghavantv0

Just to be quite clear: If you want to do this using the tools (described in answers below) on Galaxy main, you will do it all via a web browser so the operating system and CPU architecture of the PC running the web browser is irrelevant - just so long as it's a w3c standards compliant browser like firefox or chrome it will work fine.

ADD REPLYlink written 2.9 years ago by fubar1.1k

Thank you for your reply, I mentioned that my computer is 32 bit because I found that many of the versions of SRAtool kit works only in 64 bit. I did not see any options in galaxy for converting SRA to FASTAQ.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by rahulraghavantv0

Please see the first reply I sent about the Galaxy version of the tools. 

ADD REPLYlink written 2.9 years ago by Jennifer Hillman Jackson23k
1
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

To do this within Galaxy, use a local or cloud and this tool shed repository:
http://toolshed.g2.bx.psu.edu/view/matt-shirley/ncbi_sra_toolkit

If you want to do this line-command, the legacy tools can be obtained here. 32-bit is no longer supported, but seems to be available.
http://www.ncbi.nlm.nih.gov/books/NBK158900/

Best, Jen, Galaxy team

ADD COMMENTlink written 2.9 years ago by Jennifer Hillman Jackson23k

Thank you, From the link you gave me, I found that tool kit in galaxy but how do I install it ? I have decompressed the file.

ADD REPLYlink written 2.9 years ago by rahulraghavantv0

Tools from the Tool Shed are for use in a local or cloud Galaxy. You install these as the administrator directly into Galaxy. These Galaxy options are described here with further links for set-up: https://wiki.galaxyproject.org/BigPicture/Choices

ADD REPLYlink written 2.9 years ago by Jennifer Hillman Jackson23k
1
gravatar for Bjoern Gruening
2.9 years ago by
Bjoern Gruening4.8k
Germany
Bjoern Gruening4.8k wrote:

Please also have a look at the "Get data" -> "EBI SRA" data source tool. You can get a lot of SRA files from there, directly to Galaxy as FASTQ file.

Cheers,

Bjoern
 

ADD COMMENTlink written 2.9 years ago by Bjoern Gruening4.8k
0
gravatar for rahulraghavantv
2.9 years ago by
rahulraghavantv0 wrote:

Thank you very much for the reply. I have installed both SRAtoolkit and NGSFC . They are able to convert sra files to fastaq but those fastaq files are not giving me FASTA QC results in galaxy. Therefore, to confirm it I obtained a fastaq file from outside. And that fastaq file was perfectly opening in galaxy and gave me FASTA QC results. But all the fastaq files I made in my PC with NGSFC is not giving me FASTA QC results in galaxy. so what should I do now? it always shows red color error with my FASTAq files.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by rahulraghavantv0

If you are using the line-command tools from the external source, we cannot help troubleshoot that. I just included the link in case you wanted to try it and did mention that they seem to not be supported anymore by the authors (they source states that these are available "as is").

I wouldn't expect that this is the issue, but do note that Galaxy uses the file extension/format name "fastq" not "fastaq". Upload auto-detection should be able to detect the proper file type, but you could double check by using the correct extension to see if that helps.

It is not clear if you have tried the Galaxy SRA-Toolkit from the Tool Shed (used in a local or cloud Galaxy). Is this problematic? We may be able to help or you can contact the repository owner. Testing to see if other tools also function in your local/cloud would be a prerequisite to ensure there is not another problem with your basic Galaxy install/set-up.

There are a few comment threads going - I'll put in quick replies, but going forward please try to bundle followup into a single comment.

Thanks, Jen, Galaxy team

ADD REPLYlink written 2.9 years ago by Jennifer Hillman Jackson23k
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