Add T. Brucei 927 Genome To Galaxy Main?

4.9 years ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Susanne, I wasn't able to locate this exact assembly at NCBI - is it there? Is there a known reason why it isn't? We have a general guideline to include genomes that are published there, although there is some leeway for open source, finished (or at least not early stage draft) genomes from other sources. I'll need to review (credits, usage, status, etc.). Please have a look and write back with more details of what you know about this one (can be direct to me), so I don't miss anything. Thanks! Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 4.9 years ago by Jennifer Hillman Jackson ♦ 25k

Hello Jen, The Trypanosomas are sequenced by Sanger. The sequences are available at GeneDB. http://www.genedb.org/Homepage/Tbruceibrucei927 ftp://ftp.sanger.ac.uk/pub/pathogens/Trypanosoma/brucei/Latest_Whole_G enome_Sequence/Tb927_v5.2_20131108/fasta/ I work with EuPathDB (http://eupathdb.org) and some of our users are having trouble uploading larger BAM files onto our GBrowse instance. I thought it would be good to help our users convert their data into smaller file formats using Galaxy. I'm such a novice with that sort of thing, it's been good to have your help. Susanne Susanne Warrenfeltz, PhD EuPathDB Outreach http://eupathdb.org Follow us on twitter: http://twitter.com/eupathdb FaceBook: https://www.facebook.com/pages/EuPathDB/133123003429972 To: Susanne Warrenfeltz; 'galaxy-user@lists.bx.psu.edu' Subject: Re: [galaxy-user] add T. brucei 927 genome to Galaxy main? Hi Susanne, I wasn't able to locate this exact assembly at NCBI - is it there? Is there a known reason why it isn't? We have a general guideline to include genomes that are published there, although there is some leeway for open source, finished (or at least not early stage draft) genomes from other sources. I'll need to review (credits, usage, status, etc.). Please have a look and write back with more details of what you know about this one (can be direct to me), so I don't miss anything. Thanks! Jen Galaxy team It would be very nice to see the Trypanosoma brucei TREU927 genome added to Galaxy: http://tritrypdb.org/common/downloads/Current_Release/TbruceiTREU927/f asta/data/TriTrypDB-6.0_TbruceiTREU927_Genome.fasta Thanks Susanne ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD REPLY • link written 4.9 years ago by Susanne Warrenfeltz • 40

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