Anyone has tools for NCBI Lite-SRA format ?
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
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 <gordon@cshl.edu> 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:
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
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
participants (3)
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anton -
Assaf Gordon -
Stephen Taylor