Anyone has tools for NCBI Lite-SRA format ?

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Anyone has tools for NCBI Lite-SRA format ?

Assaf Gordon-2
Hi all,

Does any one have (or galaxy team: are you planning to develop) tools for NCBI's SRA binary container format ?

For starters, a wrapper for the "fastq-dump" program that converts a lite-sra back to fastq ?

Just trying to avoid re-inverting a wheel,
 -gordon
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Re: Anyone has tools for NCBI Lite-SRA format ?

Anton Nekrutenko
Assaf:

We are getting multiple requests for this but did not have the bandwidth to do it.  So if you are planning to implement - share through the toolshed and we will roll it to main.

Tx,

Anton

http://usegalaxy.org

On Apr 1, 2011, at 6:09 PM, Assaf Gordon <[hidden email]> wrote:

> Hi all,
>
> Does any one have (or galaxy team: are you planning to develop) tools for NCBI's SRA binary container format ?
>
> For starters, a wrapper for the "fastq-dump" program that converts a lite-sra back to fastq ?
>
> Just trying to avoid re-inverting a wheel,
> -gordon
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/

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Re: Anyone has tools for NCBI Lite-SRA format ?

Assaf Gordon-2
anton wrote, On 04/01/2011 09:02 PM:
> We are getting multiple requests for this but did not have the
> bandwidth to do it.  So if you are planning to implement - share
> through the toolshed and we will roll it to main.
>

To start, this patch adds "SRA" binary type with sniffing and upload support:
http://cancan.cshl.edu/labmembers/gordon/files/sra_binary_data_type.patch


It only adds the datatype to "datatypes_conf.xml.sample", so existing installations must manually add the following lines to their ""datatypes_conf.xml":
<datatype extension="sra" type="galaxy.datatypes.binary:Sra" mimetype="application/octet-stream" display_in_upload="true"/>

and

<sniffer type="galaxy.datatypes.binary:Sra"/>



A question to people who are using "fastq-dump" on the command line:
What are the most common parameters you're using ?
I've heard about using Illumina or Sanger quality scale (-Q 64 / -Q 33),
Minimal read length (-M),
Clipping (-W),
quality filtering (-E).

Suggestions are very welcomed.

-gordon

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Re: Anyone has tools for NCBI Lite-SRA format ?

Stephen Taylor
Hi,

>> We are getting multiple requests for this but did not have the
>> bandwidth to do it.  So if you are planning to implement - share
>> through the toolshed and we will roll it to main.
>>
>

The way I got round this was let the SRA website do the conversion. So just paste in the URL in the upload screen:

http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=dload&run_list=SRRXXXXXX&format=fastq

Where SRRXXXXXX is the archive of interest, and it downloads Sanger FASTQ sequences to Galaxy.

Regards,

Steve
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