Re: [galaxy-user] extract genome sequence
Hi Yan, Both of the other suggestions are good - I'll also give you another choice to build coordinates before using the "Fetch Sequences -> Extract Genomic DNA" tool to obtain the fasta sequence. Using your input in BED/Interval format (convert from GFF/GTF if necessary, using the tool "Convert Formats -> GFF-to-BED "), or the first 6 columns if a BED12 (use "Cut" as needed), then run the "Operate on Genomic Intervals -> Get flanks" tool. "Region:" Whole feature "Location of the flanking region/s:" Both "Offset" 0 "Length of the flanking region(s):" 5000 Your question is similar to this one (the first part, but I thought you might be interested in how to just get the flanks, too). http://user.list.galaxyproject.org/Get-flanks-version-1-0-0-td4604849.html Good luck with your project! Jen Galaxy team ps. To search prior questions, please see: http://galaxy.psu.edu/search/mailinglists/ On 9/23/12 7:00 PM, Yan He wrote: Hi everyone, I have the genome sequence and gene annotation file. Is there a tool on Galaxy to extract the 5,000 bp upstream, 5,000 bp downstream and genome sequences of the genes (including exons and introns) from the genome sequence? Any suggestions are highly appreciated! Thanks! Yan ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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/
Re: [galaxy-user] extract genome sequence
Yan, One way to do this is to create an interval file with the new co-ordinates (+/- 5kb) and then use the Fetch Sequences > Extract genomic DNA tool. To create a new co-ordinates file, input your annotation file into the Text Manipulation > Compute tool, using expressions like "c3 = c3-5000" to get your new co-ordinates. You'll get 2 new columns in the final output file and then use the Text Manipulation > Cut tool to extract the columns you need to create an interval file. Hope this helps. Cheers, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 On 24/09/2012 09:02, "Björn Grüning" wrote: >Hi Yan, > >did you know the tool extractfeat from the EMBOSS suite (its in the >toolshed)? > >I don't know offhand if it can work in batch mode, but its possible to >add that feature. > >Cheers, >Bjoern > >> Hi everyone, > >> I have the genome sequence and gene annotation file. Is there a tool >> on Galaxy to extract the 5,000 bp upstream, 5,000 bp downstream and >> genome sequences of the genes (including exons and introns) from the >> genome sequence? Any suggestions are highly appreciated! Thanks! >> >> >> >> Yan >> >> >> ___ >> 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/ > >-- >Björn Grüning >Albert-Ludwigs-Universität Freiburg >Institute of Pharmaceutical Sciences >Pharmaceutical Bioinformatics >Hermann-Herder-Strasse 9 >D-79104 Freiburg i. Br. > >Tel.: +49 761 203-4872 >Fax.: +49 761 203-97769 >E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de >Web: http://www.pharmaceutical-bioinformatics.org/ > >___ >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/ ___ 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/
Re: [galaxy-user] extract genome sequence
Hi Yan, did you know the tool extractfeat from the EMBOSS suite (its in the toolshed)? I don't know offhand if it can work in batch mode, but its possible to add that feature. Cheers, Bjoern > Hi everyone, > I have the genome sequence and gene annotation file. Is there a tool > on Galaxy to extract the 5,000 bp upstream, 5,000 bp downstream and > genome sequences of the genes (including exons and introns) from the > genome sequence? Any suggestions are highly appreciated! Thanks! > > > > Yan > > > ___ > 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/ -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/ ___ 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/
