[galaxy-user] cufflinks
On 7/1/12 8:30 PM, Paul Hello Jennifer, I was hoping you could enlighten me about a problem I am currently having. I have two rna-seq datasets that I am trying to evaluate using cufflinks - I keep getting null sets back with the second set, no matter what I do. I am pretty sure that the data are identical in nature, just from different conditions. Is there an issue with the current cufflinks instance? Or am I screwing up somehow. I am trying to evaluate item 149 from my history (which is the filtered and sorted set from Bowtie analysis). This should be identical in nature to item 113, with the only difference being the read source (same bug, different conditions). Both were mapped to the same ref genome (from the history) and the same annotation file (again, from the history). Any help is much appreciated! -- Paul -- 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/
[galaxy-user] request for a new genome (Aedes aegypti)
Dear Galaxy team, I would like you to add in the insect genomes available in Galaxy the genome of Aedes aegypti which is available in Vectorbase (http://aaegypti.vectorbase.org/), Thank you, Laurence Després -- Laurence Després Laurence Després Equipe Bases Génétiques de l'adaptation (GBA) Laboratoire d'Ecologie Alpine (LECA) UMR CNRS 5553 Université J. Fourier Domaine universitaire de Saint Martin d'Hères 2233, rue de la piscine Bât. D BiologieBP 53, 38041 Grenoble Cedex 9, France laurence.desp...@ujf-grenoble.fr mailto:laurence.desp...@ujf-grenoble.fr Tel: 33 (0)4 76 63 56 99 Fax: 33 (0)4 76 51 42 79 http://www2.ujf-grenoble.fr/leca/ Master2R Biodiversité-Ecologie-Environnement (BEE) http://www-biologie.ujf-grenoble.fr/SiteBio/ http://www-biologie.ujf-grenoble.fr/SiteBio/articles.php?lng=frpg=280 ___ 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] cufflinks
Hello Paul, By null values I am guessing that you mean that the FPKM values are 0. http://cufflinks.cbcb.umd.edu/manual.html#transexpr This is an indication of a possible mismatch between the input BAM/SAM data and the reference annotation GTF file. You will need to double check that both of these are true between all inputs: 1 - the chromosome naming is identical 2 - the sort ordering is identical Our RNA-seq FAQ has items that cover both: https://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq If that does not resolve the issue, and there is no error dataset from Galaxy, you might consider the Cufflinks help email address next: tophat.cuffli...@gmail.com http://wiki.g2.bx.psu.edu/Support#Interpreting_scientific_results (see Example: unexpected results with RNA-seq analysis tools.) Best, Jen Galaxy team I was hoping you could enlighten me about a problem I am currently having. I have two rna-seq datasets that I am trying to evaluate using cufflinks - I keep getting null sets back with the second set, no matter what I do. I am pretty sure that the data are identical in nature, just from different conditions. Is there an issue with the current cufflinks instance? Or am I screwing up somehow. I am trying to evaluate item 149 from my history (which is the filtered and sorted set from Bowtie analysis). This should be identical in nature to item 113, with the only difference being the read source (same bug, different conditions). Both were mapped to the same ref genome (from the history) and the same annotation file (again, from the history). Any help is much appreciated! -- Paul -- 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] request for a new genome (Aedes aegypti)
Hello Laurence, The genome Mosquito (Aedes aegypti) (AaegL1) is already included in Galaxy as a native genome. To location the genome, type part of the name, I used parts of both the common name mos and the scientific name aeg and found the genome on the Edit attributes page (pencil icon) and on tool forms (Bowtie, BWA, TopHat). AaegL1 is the latest genome build. There are more recent gene builds, but these refer to annotation, not reference sequence. If you wish to use the most current gene build annotation information, this appears to be available through Biomart, which means that the Galaxy Get Data - Biomart tool can be used to import the datasets directly for use with tools. Hopefully this helps, Jen Galaxy team On 7/2/12 7:53 AM, Laurence Després wrote: Dear Galaxy team, I would like you to add in the insect genomes available in Galaxy the genome of Aedes aegypti which is available in Vectorbase (http://aaegypti.vectorbase.org/), Thank you, Laurence Després -- Laurence Després Laurence Després Equipe Bases Génétiques de l'adaptation (GBA) Laboratoire d'Ecologie Alpine (LECA) UMR CNRS 5553 Université J. Fourier Domaine universitaire de Saint Martin d'Hères 2233, rue de la piscine Bât. D BiologieBP 53, 38041 Grenoble Cedex 9, France laurence.desp...@ujf-grenoble.fr mailto:laurence.desp...@ujf-grenoble.fr Tel: 33 (0)4 76 63 56 99 Fax: 33 (0)4 76 51 42 79 http://www2.ujf-grenoble.fr/leca/ Master2R Biodiversité-Ecologie-Environnement (BEE) http://www-biologie.ujf-grenoble.fr/SiteBio/ http://www-biologie.ujf-grenoble.fr/SiteBio/articles.php?lng=frpg=280 ___ 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/
[galaxy-user] Initial QC and grooming for Illumina HiSeq2000 paired end RNAseq data
I am trying to do RNAseq analysis on Paired end data from the Hiseq2000. I have about 50 files for each sample (25 forward and 25 reverse - although each sample has a different number of files). I think that I need to: -convert them into FASTQ sanger format using the FASTSQ groomer tool -check the quality using the FASTQqc tool I don't know how to handle this many files. Do I have to groom and run the QC for each file? Should I join the paired files and run both tools on each pair, or should I combine all of the data for each sample (which I don't know how to do) and then groom and run the QC for all of the reads for the sample. Thanks in advance for advice Lindsey ___ 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] GMOD Summer School application deadline
Hello, The deadline to apply for the GMOD Summer School is in one week, July 9th. The application is available as a Google Form: https://docs.google.com/spreadsheet/embeddedform?formkey=dG5hNGFiQ3UwYTV2LUZxZW04Qm1yZXc6MQ In the GMOD Summer School (August 24-29, 2012) we will cover the installation, configuration and use of a variety of GMOD tools, including Chado, GBrowse, JBrowse and Galaxy. For more information on the course, see the course web page at http://gmod.org/wiki/2012_GMOD_Summer_School The course will make heavy use of the Amazon Web Service (aka, the Cloud) via a grant from Amazon. Enrollment is limited to 24 students, and the application process is competitive: the last few years we've received over 75 applications for those 24 spots. I look forward to seeing you in North Carolina in August! -- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ___ 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/
