Question: How to convert SRA Files to FASTAQ files in a 32 BIt windows computer ( beginner here)
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rahulraghavantv • 0 wrote:
How to convert SRA Files to FASTAQ files in a 32 BIt windows computer ( beginner here)
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Jennifer Hillman Jackson ♦ 25k 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
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.
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
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Bjoern Gruening ♦ 5.1k 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
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rahulraghavantv • 0 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.
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
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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.
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.
Please see the first reply I sent about the Galaxy version of the tools.