downloading reference sequences and other questions
Hi I have a few questions 1. I am trying to use Bowtie to map my data using a reference genome. the genome is available on Galaxy (Escherichia coli DH10B (20079)). Is there a way that I can download the file in fasta format to use as a reference in Tablet? I can import the SAM output into Tablet if I do not give it a reference, but I would like to see it with the reference 2. I have used the Sam to Bam converter and downloaded the file to my computer then tried to import it into Tablet, but it gives an error. Does anyone have any advice on doing this? 3. Does Galaxy have any tools for doing a blast search against a reference genome or database? Any help/instructions that you point me to is greatly appreciated. Jo
Joanne: 1. There is no mechanism for downloading reference sequences from Galaxy at this time. 2. I am not sure what you mean by 'Tablet'. 3. Megablast tool ('NGS: Mapping -> Megablast') will allow you to perform comparisons against nt, wgs, and htgs databases. Thanks for using Galaxy, anton galaxy team Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org On Jun 22, 2011, at 4:15 PM, Joanne Rampersad wrote:
Hi I have a few questions
1. I am trying to use Bowtie to map my data using a reference genome. the genome is available on Galaxy (Escherichia coli DH10B (20079)). Is there a way that I can download the file in fasta format to use as a reference in Tablet?
I can import the SAM output into Tablet if I do not give it a reference, but I would like to see it with the reference
2. I have used the Sam to Bam converter and downloaded the file to my computer then tried to import it into Tablet, but it gives an error. Does anyone have any advice on doing this?
3. Does Galaxy have any tools for doing a blast search against a reference genome or database?
Any help/instructions that you point me to is greatly appreciated.
Jo ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hello Jo, Please see below On 6/22/11 1:15 PM, Joanne Rampersad wrote:
Hi I have a few questions
1. I am trying to use Bowtie to map my data using a reference genome. the genome is available on Galaxy (Escherichia coli DH10B (20079)). Is there a way that I can download the file in fasta format to use as a reference in Tablet?
I can import the SAM output into Tablet if I do not give it a reference, but I would like to see it with the reference
Galaxy does not currently have genomes available for download. Good sources would be UCSC, NCBI, Ensembl, and other species-specific projects.
2. I have used the Sam to Bam converter and downloaded the file to my computer then tried to import it into Tablet, but it gives an error. Does anyone have any advice on doing this?
The best folks to answer Tablet questions would be those tool authors, but that said, a some guesses are that the .bam.bai index file was not loaded along with the .bam? Or maybe the SAM needed to be sorted in some special way first?
3. Does Galaxy have any tools for doing a blast search against a reference genome or database?
BLAST is not in on the Galaxy main server, but if you want to see how it is incorporated, it is on our test server (but beware if running any serious jobs, this is an active development area and large runs are not permitted). http://test.g2.bx.psu.edu. After testing out the implementation, and you decide that you want to run BLAST on full datasets using Galaxy, then creating a cloud or local instance is the recommendation. http://getgalaxy.org http://getgalaxy.or/cloud Hopefully this is helpful! Thanks for using Galaxy! Best, Jen Galaxy team
Any help/instructions that you point me to is greatly appreciated.
Jo ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/
Link correction:
should be http://usegalaxy.org/cloud With the two answers from our team to (hopefully) help, we wish the best for your project, Jen Galaxy team
participants (3)
-
Anton Nekrutenko -
Jennifer Jackson -
Joanne Rampersad