Multiple Blast Search

Question: Multiple Blast Search

8.2 years ago by

Wong, Chloe • 20 wrote:

Hi, I am new to Galaxy and would like to say thanks for the very useful introduction video. I would like to map ~26,000 sequence on the human genome and I think I could possibly use Galaxy to do it. I managed to get data from the UCSC as the reference genome and have also loaded up my file containing the sequence that I would like to map. However I am unsure how I could align the two files. I thought maybe I could use the 'fetch alignment' tool to perform a blast search but don't think it worked. Can you please let me know if it's possible to use Galaxy for this job? and if so, can you give me some ideas/example of how I can achieve this? Thanks very much for your help in advance! Chloe Chloe Wong PhD Student MRC SGDP Research Centre, Insitute of Psychiatry, King's College London, De Crespigny Park, Denmark Hill, London SE5 8AF Tel: +44(0)20 7848 5410

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modified 8.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 8.2 years ago by Wong, Chloe • 20

8.2 years ago by

Kevin • 150

Kevin • 150 wrote:

Hi Chloe do u mean to use the NGS mapping portion of galaxy? U dint mention ur input files are in what format Sent from my iPod

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8.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Chloe, Under the tool group "NGS: Mapping" are alignment tools. http://usegalaxy.org/u/aun1/p/ngs-analysis-service To add/use more alignment tools in your own Galaxy instance (BLAT, BLAST, etc), instructions for set up are the Galaxy Wiki. http://bitbucket.org/galaxy/galaxy- central/wiki/ISMB2010_GalaxyTutorial_3_RunningYourOwn You also have the option to run the alignment externally (line command or other) and then to upload the results into the Galaxy main site for further analysis. Hopefully one of these options will work for you. Other solutions for running large jobs are available (ex: using a cloud). Please let us know if this is something you would like help with. Best, Jen Galaxy Team -- Jennifer Jackson http://usegalaxy.org

ADD COMMENT • link written 8.2 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks very much Jennifer! Chloe _______________ To: Wong, Chloe Cc: galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] Multiple blast search Hello Chloe, Under the tool group "NGS: Mapping" are alignment tools. http://usegalaxy.org/u/aun1/p/ngs-analysis-service To add/use more alignment tools in your own Galaxy instance (BLAT, BLAST, etc), instructions for set up are the Galaxy Wiki. http://bitbucket.org/galaxy/galaxy- central/wiki/ISMB2010_GalaxyTutorial_3_RunningYourOwn You also have the option to run the alignment externally (line command or other) and then to upload the results into the Galaxy main site for further analysis. Hopefully one of these options will work for you. Other solutions for running large jobs are available (ex: using a cloud). Please let us know if this is something you would like help with. Best, Jen Galaxy Team -- Jennifer Jackson http://usegalaxy.org

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