Re: [galaxy-user] embl 66 genome for RNAseq analysis
Hello Karthik, Because it is sourced from UCSC, the GRCh37 genome is available in Galaxy as hg19. The full name is: Human Feb. 2009 (GRCh37/hg19) (hg19) This aligns with how Ensembl also understands the content: http://lists.ensembl.org/pipermail/dev/2012-February/002180.html For RNA-seq analysis (and sometime other types of analysis) you may need to adjust other input data's chromosome naming to match the UCSC format. This is explained in the RNA-seq FAQ: https://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq5 The data in the FTP link you provide is annotation data. To use annotation data with the RNA-seq pipeline, a GTF file would be a good format. The RNA-seq tool pages have a link out to Ensembl, but any source from the same genome is OK (UCSC, etc.). Best, Jen Galaxy team On 4/2/12 4:14 AM, Karthik Srinivasan wrote: Hi, How do I run Tophat and RNA-Seq analysis using the GRCH37- embl 66 genome? I noticed there is no input for this genome version. Can I construct a reference genome from the following embl format source sequences: ftp://ftp.ensembl.org/pub/release-66/embl/homo_sapiens/, and map it against my RNAseq data? Regards, Karthik Karthik Srinivasan | Senior Application Engineer P:+912242554282 tel:+912242554282 | M:+919987014704 tel:+919987014704 OracleHealth Sciences Global Business Unit 6'th Floor, Silver Metropolis, W.E.Highway, Goregaon(E) | 400063 Mumbai ___ 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/
[galaxy-user] USing GATK DepthOfCoverage with all exon enriched data
Hi, I have NGS results of DNA enriched for exons with an AllExon kit (Agilent). I have a bed file with the list of targeted sequences. I want to use GATK DepthOfCoverage to compare the results to the bed file and to get all the targets that were covered by n reads. How can I do that with Galaxy on the web? or in Amazon? My question has 2 parts: 1. How can I specify the target intervals in Galaxy on the web? (the -L command in Unix commandline) 2. How can I ask the coverage for single bases instead of statistics? Thanks, Lilach ___ 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/
[galaxy-user] Google Summer of Code 2012 - Application Deadline on Friday 6th
The Genome Informatics group http://gmod.org/wiki/GSoC, is taking part in the Google Summer of Code (GSoC) http://code.google.com/soc/ program. This year, the Genome Informatics group, will be organizing the joint efforts of Galaxy http://galaxy.psu.edu/, GBrowse http://gbrowse.org/index.html, Generic Model Organism Database (GMOD) http://gmod.org/, JBrowsehttp://jbrowse.org/ , Reactome http://www.reactome.org/, Wormbase http://www.wormbase.org/, and PortEco http://porteco.org/. GSoC is a global program that funds student programmers around the world to write code for open source projects. More information about our project ideas and the GSoC program is available on the GMOD website http://gmod.org/wiki/GSoC. If you are a student interested in coding for our open source projects, then check out the links above and submit your project proposal as soon as possible. The application deadline is 6th April 2012. Robin Haw Genome Informatics Group Admin http://gmod.org/wiki/GSoC ___ 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/
[galaxy-user] Generating gff file
Hi, Is it possible to generate gff file in galaxy which I can use in Seqmonk? Abdullah -- Abdullah Al Mahmud, PhD Postdoctoral fellow University of Montreal Lab of Dr. Jacques Michaud CHU Sainte-Justine Research Center, 3175, Cote-Sainte-Catherine, A-709 Montreal, Quebec, H3T 1C5, Canada. abdullah.al.mah...@umontreal.ca ___ 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/
[galaxy-user] Disk space quota Issue
Dear Administartor My disk space quote is full, is their any way to increase it,or only way is delete some files... Best Ateeq Ateequr Rehman House No. 2 ground floor Blauenstr. 10 79115 Freiburg im Breisgau ___ 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/
[galaxy-user] BWA in Galaxy
Is it possible to align FASTq reads from Illumina Hi-seq reads to human genome in Galaxy? I see only Bowtie/ I guess next question will be how different is Bowtie from BWA? I want to find out sequence variations. Thanks ___ 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/
