The patches are just representing alternate paths (not all are truly haplotypic). Some of these represent corrections to the underlying chromosome assembly. Basically, regions where the chromosome tiling path is wrong. We release the fixes ahead of the next build to make them accessible to folks.
Deanna On 6/10/11 8:43 AM, "Will McLaren" <w...@ebi.ac.uk> wrote: >Hi David, > >You can find information about the assemblies here: > >http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtml > >The patches so far have just included extra regions representing >alternative haplotype regions (e.g. MHC). > >Ensembl 62 was released on patch 3: > >http://www.ensembl.org/Homo_sapiens/Info/Index > >If your data uses only to the reference chromosomes then you should >have no issues using hg19 or any of the patches released so far. > >Cheers > >Will McLaren >Ensembl Variation > >On 10 June 2011 12:21, David Matthews <d.a.matth...@bristol.ac.uk> wrote: >> Dear Galaxy-users, >> Does anyone know what the differences are between hg19 and hg19patch2 >>and >> can anyone tell me if the latest ensembl gtf file (v62) is definitely >> compatible with both hg19 and hg19patch2? >> >> >> Best Wishes, >> David. >> __________________________________ >> Dr David A. Matthews >> Senior Lecturer in Virology >> Room E49 >> Department of Cellular and Molecular Medicine, >> School of Medical Sciences >> University Walk, >> University of Bristol >> Bristol. >> BS8 1TD >> U.K. >> Tel. +44 117 3312058 >> Fax. +44 117 3312091 >> d.a.matth...@bristol.ac.uk >> >> >> >> >> >> On 10 Jun 2011, at 11:39, Michal Stuglik wrote: >> >> >> Hi Jen, >> >> It works, thanks! >> >> I am wondering why using Text Manipulation/Compute function, galaxy >>changes >> brackets '[' to '__ob__' and '__cb__' for ']', so for this: >>str(c1)[1:2] --> >> str(c1)__ob__1:2__cb__ >> >> thanks a lot, >> michal >> >> Hi Michal, >> >> The tool "Fetch Sequences -> Extract Genomic DNA" can be used to extract >> fasta sequences. The coordinates can be BED, GTF, etc. and the "genome" >> doesn't necessarily have to be an actual genome, just a fasta file in >>your >> history. >> >> To subset a data string, the tool "Text Manipulation -> Trim" might be >> helpful. This would only work if you want to use the same rules for an >> entire file (or split your file up and run the tool on those subfiles >>using >> different rules). Practical for some cases, but not all. >> >> And the final option is for coordinate data - tools in "Operate on >>Genomic >> Intervals". Once you have the final coordinate set, going back and >>using the >> "Fetch Sequences" tool can capture the associated result fasta sequence, >> from a native genome or a fasta file in your history, as described >>above. >> >> Hopefully this gives you an option that will work for your project, >> >> Best, >> >> Jen >> Galaxy team >> >> On 6/5/11 7:14 AM, Michal Stuglik wrote: >> >> Hi all, >> >> I am wondering if galaxy has tool to substring/extract sequence/text >> from another sequence/text based on coordinates in columns (start, end >> column) or how to do it in Text Manipulation/Compute? >> >> all the best, >> michal >> >> >> ___________________________________________________________ >> 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/ >> > >___________________________________________________________ >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/
