April 2011 - galaxy-user - lists.galaxyproject.org

Bowtie vs TopHat
by vasu punj 09 Apr '11

09 Apr '11

I have a question on using Bowtie vs TopHat. I do understand that TopHat call Bowtie and if followed by cufflink and cuffdiff will give transcript differential expression etc. and most of reads will be mapped to exons across junctions. Anyone has tried using Bowtie with same reads and will there be any difference in alignemnts? Theroetically, I would consider when Bowtie is used it will align the reads to human genome at various locations not only across junsctions and the pattern may be different from TopHat alignment. I ran such experiment but dont find much of difference in pattern of alignments? Before I share my project I just want to have feedback from other users about their experience of using Bowtie vs TopHat for alignments. Thanks.

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April 8, 2011 Galaxy Development News Brief
by Jennifer Jackson 09 Apr '11

09 Apr '11

April 8, 2011 Galaxy Development News Brief http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_… Prior releases: https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBriefs ------------ 2011_04_08 Highlights Workflow API Move Data Library Items 10 New Genomes & 29 New LiftOver Import Workflows & Histories ClustalW Multiple-Seq Alignments & Sequence Logos Major Trackster Visualization Improvements ------------ How to get this distribution https://bitbucket.org/galaxy/galaxy-dist/ new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 50e249442c5a ------------ Key Upcoming Galaxy Events May 24-26, 2011 Galaxy Community Conference, Lunteren, The Netherlands. http:galaxy.psu.edu/gcc2011/ April 24 is the Early registration deadline (save 20%!) http://galaxy.psu.edu/gcc2011/Register.html April 13-14, NBIC Galaxy Hackathon, Belgium. Please submit your suggestions! http://wiki.nbic.nl/index.php/NBIC_Galaxy_Hackathon_project ------------ What's New Workflow API An API for executing workflows has been added. Usage examples /scripts/api/workflow_execute.py /scripts/api/example_watch_folder.py. Move Data Library Items We have introduced a feature that enables you to move library datasets or folders (including all folder contents) to other locations within the same data library or to a different data library altogether. Galaxy administrators can perform this feature on any data library item and can move items to any data library. Users that are not Galaxy administrators must be given the modify library item permission on an item in order to move it, and they'll need the add library item permission on the desired target data library folder in order for it to be displayed in the select list of targets. Moving a single dataset To move a single dataset, select the Move this dataset option from the dataset's pop-up menu. http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011… The default behavior is to move items to other locations within the same data library, so you'll initially be presented with a list of valid folders from which to choose for the new target location. http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011… After selecting the desired folder, clicking the Move button will move the dataset to the selected folder. Moving a Folder Moving a folder is very similar to moving a single dataset - just select the Move this folder option from the folder's pop-up menu. http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011… To move the folder to a different data library, after selecting the Move this folder option, click the Choose another data library link on the Move data library items page. The folders select list will change to a select list of data libraries to which you are authorized to move the item. When you select a target data library, the select list will change again to display the list of folders in the selected data library to which you are authorized to move the item. Clicking the Move button will move the folder and all of it's contents to the selected target folder within the selected target data library. The target folders select list is filtered to included only valid folders to which you can move the item. For example, you cannot move a folder to one of it's own sub-folders in one step. To do this, the sub-folder must be moved outside of it's parent, and then the parent can be moved to the folder that it previously contained. http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011… ------------ Updated & Improved Data Content * Genomes o New & included in NGS Tools + Saccharomcyes cerevisiae: Saccharomcyes_cerevisiae_S288C_SGD2010 + Arabidopsis lyrata: Araly1 + Purple Sea Urchin: strPur3 and Spur_v2.6 + Hydra: Hydra_JCVI + Zebrafish: danRer7 + Poplar: Ptrichocarpa_156 + Chimpanzee: panTro3 + Northern White-Cheeked Gibbon: nomLeu1 + Korean Man AK1: Homo_sapiens_AK1 o New & not included in NGS Tools + Caenorhabditis remanei: caeRem2 o Existing genomes added to NGS Tools + hg19 Canonical female (no Y chromosome) + Streptococcus pneumoniae R6: 278 + Drosophila virilis: droVir3 and droVir2 * New LiftOver Files o caeRem2 --> caePb1, caeRem2 --> caeRem3, caeRem2 --> cb3, caeRem2 --> ce4, caeRem2 --> priPac1, calJac3 --> hg18, canFam2 --> monDom5, danRer6 --> danRer7, danRer7 --> fr2, danRer7 --> gasAcu1, danRer7 --> hg19, danRer7 --> mm9, danRer7 --> oryLat2, danRer7 --> panTro3, danRer7 --> tetNig2, danRer7 --> xenTro2, droVir3 --> droVir2, fr2 --> danRer7, gasAcu1 --> danRer7, hg18 --> calJac3, hg19 --> danRer7, mm9 --> danRer7, panTro3 --> danRer7, panTro3 --> hg19, ponAbe2 --> calJac3, ponAbe2 --> monDom5, strPur2 --> ci2, tetNig2 --> danRer7, xenTro2 --> danRer7 * Add Genomes to Your Instance http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup * Current Galaxy Main Genomes http://bitbucket.org/galaxy/galaxy-central/wiki/GenomeData Current Tools * Add more verbose error reporting to FASTQ Groomer tool. Provides more information to allow users to determine what is wrong with FASTQ files with invalid format. * Enhance Bowtie wrapper to accept non-Sanger variant FASTQ files. * Allow Upload Tool to function on https URLs. * Add count GFF features tool and tests: o Filter and Sort --> GFF --> Filter GFF file by feature count using simple expressions. o Tool counts the number of features in a GFF file. Note: this is different than the number of lines because a single GFF feature can often span multiple lines. * Tophat v1.2.0 support: o (a) allow indel search. o (b) max insertion and max deletion lengths. o (c) library type. * Updated gff_filter_by_feature_count tool now accepts and correctly handles all GTF, GFF, and GFF3 files. * Changes for detecting and loading BAM data type Samtools version 0.1.13 or newer produces an error condition when attempting to index an unsorted BAM file. To determine if a BAM file is sorted, we first use Samtools to check the headers. If this does not provide a definitive answer and Samtools version 0.1.13 or newer is being used, we index the BAM file to see if it produces the error. This process provides a more robust approach to determining if the BAM file is sorted. New Tools * Multiple Alignments: ClustalW multiple sequence alignment program for DNA or proteins. * Motif Tools: Sequence Logo generator for FASTA data (example: ClustalW alignment). o Both tools originated from the Community Tool Shed (see below). o The Sequence Logo tool uses Weblogo3 wrapped into Galaxy to generate a sequence logo. The input file must be a FASTA file in your current history. It is recommended for viewing multiple-sequence alignment output from the ClustalW tool. Set the ClustalW output to FASTA to create the input for this tool. A typical output looks like this: http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011… Community Tools (Tool Shed) * Tuning: Clarified what is being searched in the Tool Shed. * New ClustalW wrapper (see http://www.clustal.org) for protein/dna multiple alignments based on the Galaxy ClustalW wrapper posted by Hans-Rudolf Hotz in an email on the developer list. http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html * New Weblogo3 wrapper (http://weblogo.berkeley.edu) that creates sequence logos from FASTA data such as the output from a ClustalW alignment. Data Libraries * Disabled problematic eager loading on data libraries. Very large data libraries will load two to three times quicker. * Upload Improvement with example walk-through: Uploading data library datasets 1. Apply a corrected version of the patch from Peter Cock that flips the "Preserve directory structure?" setting when uploading library datasets from filesystem paths. The checkbox is now "yes" instead of the original "no", and is checked by default. http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011… 2. Flip the behavior of the "Copy data into Galaxy" feature when uploading library datasets (similar to 2 above) to be more clear and logical. Instead of a single checkbox, this is now a select list with clearly defined options. The default setting is to copy the files into the configured Galaxy file store. http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011… 3. Allow importing items from a history to replace a library dataset with a new version. Previously, you could only replace a library dataset with a new version by uploading a single file. http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011… Workflows * Users can now import copies of their own Workflows and Histories. Trackster * Enhancements: o Implemented a data manager for Trackster and drawing is now completely tracked and controlled. o Put show_insertions and show_differences in read track config. o Filtering now supports: + (a) score columns in BED and GFF. + (b) GTF attributes. o Added BED and GFF support to visual analytics framework, and enable GOPS intersect and subtract tools to work with visual analytics. * Improvements: o Insertions and deletions now shown in reads. o Save and restore mode for feature and read tracks. o Bug fixes for drawing feature tracks in Squish and Dense mode. o Menus and menu items now work correctly. o Remove form from navigation controls so that enter key works properly and sets the chrom/low/high. o Enable full keyboard navigation via arrow keys. * Bug fixes: o Fix issues with navigation input: + (a) arrow keys no longer perform navigation + (b) invalid chromosome names are handled well. o Fix feature track bugs so that intervals are correctly drawn as half-open. o Use gap to correctly position read connector in Pack mode. o Fix read id bug in Trackster BAM data provider. Example of Trackster visualization: Track of reads mapped using Tophat (spliced) including the transcript assembled from those reads. http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011… User Interface (UI) * SGD Yeast genome added as a Gbrowse display site. * IGV added as an external display application. This is not enabled on Galaxy main, but is available for local instances. CloudMan * FTP data upload enabled. http://bitbucket.org/galaxy/galaxy-central/wiki/cloud Source * Improvements in reliability and speed regarding manipulation of instance data volumes. * The value set in 'new_file_path' in universe_wsgi.ini will now be used for creation of all temporary files. This obviates the need for setting $TEMP when running data source tools on the cluster. * Datatypes: o Add a 'subclass' flag to datatype definitions in datatypes_conf.xml that allows dynamic creation of a subclass. o Allow composite datatype datasets to be populated in the Upload tool from files that were uploaded to the Galaxy FTP server. * Tool configuration enhancements: o Allow DataToolParameter to be filtered on attributes other than dbkey (dynamic options). o Allow FromParamToolOutputActionOption and ParamValueToolOutputActionOptionFilter to access attributes of parameter values. Tool Test Framework * Specifying 'ftype="bam"' as a parameter on a test's <output> tag will now cause the test framework to use 'samtools view' to convert the file to SAM. This should make it easier to debug why the test tool output differs from your baseline test output. Test framework enhancements: * Allow toolbox tests to upload a file found located in subdirectories. * Fix a bug occurring on the determination of uploaded dataset name during the handling of the removal of .gzip or .zip extension from the uploaded filenames. * When using re_match comparison method in functional tests and line counts do not match, print out first 40 lines of the history file. Admin Menu * Add a checkbox to the Create Group page that if checked will create a new Role with the same name. This provides a similar feature the the existing checkbox on the Create Role page. * However, the behavior is now changed such that new associations are created when the checkbox is checked, whereas before, only the Group or Role objects with the same name were created, but not associated with anything. Bug Fixes * Following the login link from the Logout page no longer redirects you to the Logout page once you have logged in. * The peek setting method, set_peek(), should now function consistently across datatypes descending from Text, particularly with respect to line count estimation. * Apply patch from Ry4an Brase to correct "NoneType preference on the jobs view" issue. * Don't alter the contents of a file while uploading to a data library if using one of the Upload files from file system paths or Upload a directory of files options in conjunction with the Link to files without copying into Galaxy option. This partially resolves the issue where a supposedly sorted BAM file was being resorted upon upload to a data library when using this option. A better implementation of determining whether a BAM file has been sorted (so that it does not get resorted) remains to be done. * Extract Genomic DNA tool: o Do not fix strand for GFF input. o Handle non-GFF files when interpret features is true. * Set default value for Cuffdiff's minimum alignment count parameter to reflect v0.9.3. * Enhance GFF reader to handle headers and comments and fix bug so that new feature starts when transcript_id or gene_id changes. * Suppress most logging for Cufflinks and Cuffdiff as the logging can generate output that is incompatible with UTF-8 format used by database. * Set message type to error when history deletion fails due to sharing. * Show masthead links to Published Visualizations and Published Pages only if Tracks or Pages are enabled. * Shared visualizations work again. * Fix bug in recently used tool submenu. * Change default value for Tophat coverage search to true. ------------ About Galaxy The Galaxy team is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University. http://www.bx.psu.edu/|BX/ http://www.psu.edu/ http://www.emory.edu/ http://www.biology.emory.edu/ http://www.mathcs.emory.edu/ Galaxy is supported in part by NSF, NHGRI, the Huck Institutes of the Life Sciences, and The Institute for CyberScience at Penn State, and Emory University. http://www.nsf.gov/ http://www.genome.gov/ http://www.huck.psu.edu/ http://www.ics.psu.edu/ http://www.emory.edu/ Source http://bitbucket.org/galaxy/galaxy-central Use Galaxy! http://usegalaxy.org GalaxyProject http://galaxyproject.org Join us at Twitter #usegalaxy http://twitter.com/#!/search/galaxyproject ------------

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Re: [galaxy-user] Assemble a consensus genome from NGS data
by Benjamin Dickins 08 Apr '11

08 Apr '11

Hi David, I'm sorry for a slow response. Relatively recently I solved a problem a bit like this and would be happy to share more information with you. If your genome is small I think it makes sense to map to a reference and identify variant sites. (In my opinion de novo assembly isn't needed - see below). A basic approach is: groom FASTA file -> map with BWA -> filter SAM (uniquely mapped reads only) -> SAM-to-BAM -> Generate pileup -> Filter pileup This gives you a position-by-position summary relative to the reference. And that last step is important and needs the most care: you can have it print out differences total numbers of non-reference bases. I can share some information about thresholding how many of these constitute significant evidence that a non-reference base is actually there at that position (basically I use a binomial distribution and ask whether the distribution of ref/non-ref would occur by chance). Given that coverage of small genomes tends to be high, your first question about determining the actual genome sequence (or the quasispecies consensus if you prefer!) can be answered by majority rules: i.e., a small script (or with tools under "Text Manipulation" heading) to read off the base with the most support at each position and then to test whether that base == base in reference nucleotide column. It's probably also worth thinking about PCR duplicates (from library prep) as these could be a significant source of error, but they are also tricky when many reads will be identical anyway in the input DNA. Feel free to get in touch with me if you need a bit more clarity and/or some more specifics... cheers, Ben On Apr 4, 2011, at 9:55 PM, Anton Nekrutenko wrote: >> From: David Matthews <D.A.Matthews(a)bristol.ac.uk> >> Date: April 4, 2011 6:02:03 PM EDT >> To: galaxy-user(a)lists.bx.psu.edu >> Subject: [galaxy-user] Assemble a consensus genome from NGS data >> >> Hi, >> >> Does anyone know how to get a consensus genome from NGS data indicating the percent variance at each nucleotide? I have a small virus genome with manyfold coverage from my transcriptomic run. I'd like to know what the transcriptome indicates is the actual genome plus get a feel for any hotspots where there appears to be significant varience from the reference sequence (i.e. because the reference is wrong or perhaps because of frequent errors in that region due to RNA pol II having a problem accurately transcribing the sequence). >> >> Many thanks! >> >> David >> >> >> ___________________________________________________________ >> 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/ > Benjamin Dickins Postdoctoral Researcher Center for Comparative Genomics and Bioinformatics The Pennsylvania State University ------------------------------------------------------------ 302 Wartik Laboratory University Park, PA 16802, USA Cell/mobile: +1 814 777 1852 Office tel: +1 814 863 2185 Office fax: +1 814 865 9131 Website: http://www.bendickins.net/ Weblog: http://www.open.ac.uk/blogs/ideasblog/

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RNAseq and FPKMs per exon
by Slim Sassi 08 Apr '11

08 Apr '11

Hello, Is there a way to get FPKMs per exon? Maybe through modifying the GTF file to trick cufflinks into calculating FPKMs per exon instead of transcript or gene Thanks Slim The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Re: [galaxy-user] Analyzing Targeted Resequencing data with Galaxy
by Anton Nekrutenko 08 Apr '11

08 Apr '11

Lali: Please, always CC mailing list when you reply. > My only problem with Galaxy is that I have to keep on clearing my cache in order to get the history to display correctly, is there another way of solving this issue? Which browser/OS are your using? Thanks, anton galaxy team On Apr 5, 2011, at 11:25 AM, Lali wrote: > Thanks so much for the tips Anton! > I am very excited about the newer developments. > I did watch the quickies and they were very useful for a beginner like me, I actually did my first try at the alignment by following the Illumina single-end tutorial video step by step, but you need to watch the paired-end too, for some of the first steps, which are explained better on that one. > I have been playing around a lot with Galaxy, and I have several workflows, my department just started doing sequencing, so we don't have standard procedures set in place. I was assigned to evaluate Galaxy and CLC, and so far CLC has not impressed me, except for the fact that it can generate reports easily. > I think Galaxy is the way to go for me (us, if I can convince them to run a local server), since I am not a bioinformatician, and just the fact that you can queue up actions and just walk away is fantastic (amongst other things). > But because I am a beginner, I am not 100% of the settings I have chosen and my data is not looking too good so far, but I am having a bioinformatician come over and help me on Thursday and I think your tips will be of help. > My only problem with Galaxy is that I have to keep on clearing my cache in order to get the history to display correctly, is there another way of solving this issue? > > Best regards, > > L > > On Tue, Apr 5, 2011 at 3:56 PM, Anton Nekrutenko <anton(a)bx.psu.edu> wrote: > Lali: > > In your case the workflow for capture re-sequencing should look like this: > > 1. QC data (groom fastq files and plot quality distribution) > 2. Map the reads (use bwa) > 3. Generate and filter pileup > 4. Intersect pileup with coordinates of sure select bates. > > However, before you dive in please understand basic Galaxy functionality by taking a look at http://usegalaxy.org/galaxy101 and watching *all* Illumina-related Galaxy quickies (black boxes on the front page on Galaxy). Next, take a look at http://usegalaxy.org/heteroplasmy. > > Note, that we are working on bringing "industrial-strength" diploid genotyping functionality in Galaxy in the next two-three months that will include more sophisticated genotypers, recalibration and realignment tools, and novel visualization approaches. > > Thank for using Galaxy. > > anton > galaxy team > > > > On Apr 5, 2011, at 2:44 AM, Lali wrote: > > > Hi! > > I am having problems with my sequencing results, but I am a newbie at this; so I am thinking there is something wrong with my analysis. So far, I've tried Galaxy and CLC Workbench, but with CLC I could not align to the whole genome, only to individual chromosomes (maybe there is a way, but by the time the trial ended I had not found it). > > > > I used SureSelect capture kit and did single end sequencing on an Illumina. The files the lab sent me are FastQ Illumina 1.5 files, my samples were indexed, and I got a series of files each representing an Index. > > > > What would be the standard workflow for this kind of data? > > Which tools/settings? > > > > Does anyone have an example Galaxy workflow for preparing (clipping adapters, quality trimming) and mapping Targeted Resequencing Data? > > > > Is there a way to obtain a coverage report through Galaxy? > > > > Is it possible to ignore/discard the reads mapped when the coverage is below a certain threshold? > > > > I know, I know, a lot of things, but I am very lost. > > Any help is appreciated. > > > > L ___________________________________________________________ > > 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/ > > Anton Nekrutenko > http://nekrut.bx.psu.edu > http://usegalaxy.org > > > > Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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Re: [galaxy-user] RNA seq analysis and GTF files
by Jeremy Goecks 07 Apr '11

07 Apr '11

On Mar 31, 2011, at 12:30 PM, <ssassi(a)CCIB.MGH.HARVARD.EDU> <ssassi(a)CCIB.MGH.HARVARD.EDU> wrote: > Hi Jeremy, > I used your exercise to perform an RNA-seq analysis. First I encountered a problem where the gene IDs were missing from the results. Jen from the Galaxy team suggested this: > > "Yes, the team has taken a look and there are a few things going on. > > The first is that when running the Cuffcompare program, a reference annotation file in GTF format should be used in order to obtain the same results as in Jeremy's exercise. This seemed to be missing from your runs, which resulted in badly formatted output that later resulted in a poor result when Cuffdiff was used. > > The second has to do with the reference GTF file itself. For the best results, the GTF file must have the "gene_id" attribute defined in the 9th column of the file and the chromosome names must be in the same format as the genome native to Galaxy. Depending on the source of the reference GTF, one of these may need to be adjusted. Chromosome names can be adjusted using Galaxy's "Text Manipulation" tools. The gene_id attribute would need to be adjusted prior to loading into Galaxy. > > For mm9, using the "Get Data -> UCSC Main table browser" tool can help you to obtain all of the raw data necessary to create a complete GTF file with a gene_id identifier. Extract data from the track "RefSeq Genes" and output the primary data table "refGene" twice - first in GTF format, then again as the complete table in tabular format (not BED). Then, using your own tools, swap in the gene name from the complete table (name2 value, column 12) into the GTF file's gene_id value (which by default is the same as transcript_id). Upload and the tools will function as intended. > > The team is aware of the issues associated with GTF source files and is discussing solutions. Any changes to native data content will be reported to the mailing list in a News Brief or other communications. > > Our apologies for the inconvenience! Thanks for using Galaxy and please let us know if we can help again, > > Best, > > Jen > Galaxy team" > > > I followed the directions (or at least I think I did) and things seemed to work better but there is one more issue for example in file: > Galaxy287-[Cuffdiff_on_data_197,_data_197,_and_data_274__isoform_FPKM_tracking].tabular.txt > The column gene_short_name does not have any names in it. nearest_ref_id does have the gene ID info so I can still interpret the data, but I was wondering if there remains another problem that I'm not aware of with the GTF file. Slim, Please send questions to the galaxy-user mailing list (cc'd) rather than individual Galaxy team members; there are many people on the list that may be able to address your question, and discussions are archived for future use as well. Without seeing your analysis, I'd suggest trying two things: (1) Provide gene annotation reference file to Cufflinks as well as Cuffcompare and Cuffdiff; in other words, you'll want to do guided assembly. (2) Try using an Ensembl GTF, which has the gene name in the attributes. I think (2) is more likely to generate the results you want, but there are the many known problems in using Ensembl GTFs with Cufflinks/compare/diff. Good luck, J.

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Privacy Issues
by blake haas 07 Apr '11

07 Apr '11

Hello, Does using Galaxy through the website violate any human privacy concerns set out by the NIH, and is there any written material I could view? Is there a reason to be worried that the data can be stolen or viewed by others since it is broadcasted over the web? And is the data temporarily stored at Penn State while the analysis is occurring? Thanks for your help, Blake Haas

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Re: [galaxy-user] BED to GFF
by Jennifer Jackson 07 Apr '11

07 Apr '11

Hi Keith, Good questions - hopefully this info can help: To get from BED3 into BED12, use the BED3 as a filter in the UCSC Table Browser against a gene track (UCSC Genes, RefSeq Genes, etc.) and send the output to Galaxy. Or better, use a BED6 so that you can include strand in column 6, just enter NULL values for name (".", column 4) and score ("0", column 5) to pad the file format out correctly so that the UCSC Table Browser can interpret it. Interval is a Galaxy file type, with the UCSC Browser, the BED format must be intact and to spec. BED format is defined on the BED-to-GFF tool help (scroll down). If BED12, the features listed are interpreted from the format. If you want repeat information and such, then perhaps a tool like "Operate on Genomic Intervals -> Profile Annotations" would be a good choice. From the results, you could determine which ancillary tracks to pull over into Galaxy from the UCSC Table browser (in GTF or BED format). There are choices here (multiple repeat tracks, for example). Please note this tool is set up for human annotation currently. When running a query in the Table browser for certain data, the way the internal query is structured will pull out as a result every entry in the track with any coverage, complete (i.e. not limited to the original BED/Coordinate filters). BED3 would be necessary to pull in data contained in introns-only, although a BED6 that included strand might be a better choice for some tracks (those that are stranded). Don't use a BED12 if you want information about the entire region (transcribed & other). These "any coverage" results from UCSC can be trimmed down in Galaxy using tools in "Operate on Genomic Intervals" and "Join, Subtract and/or Group" (depends on the data). The process would be step-by-step the first time, but can be easily saved into a workflow to use again without having to re-do it each time around. If you would like more help, just let us know, Jen Galaxy team On 4/7/11 11:20 AM, Keith E. Giles wrote: > Hi Jen, > I actually used a BED3. I thought the script could go to HG18 for each > entry and then see what was there. Does the feature information need to > be in the BED file in order for it to get into the GFF file? If so, do > you know of a way to map each aligned read to a certain feature? > > On Thu, Apr 7, 2011 at 2:16 PM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hi Keith, > > Are you using a full BED12 file? Or just a BED3-6? Full BED12 should > return the available features: > > 3. feature - The name of this type of feature. Some examples of > standard feature types are "CDS", "start_codon", "stop_codon", and > "exon". > > If you would like to share a history, that would help if this is not > enough information ("Options -> Share or Publish). You can send the > link to me directly. > > Best, > > Jen > Galaxy team > > > On 4/7/11 10:46 AM, Keith Giles wrote: > > I am trying to use the galaxy "BED to GFF" function. The operation > worked, but instead of giving me back any feature information (e.g., > exon, intron, repeat, etc.); I just received back the sequence > of the > interval contained within the BED file. Does anyone know what > I'm doing > wrong? Moreover, does anyone know the best way to map each read > of a > RNAseq run to a given feature? > > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org <http://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://usegalaxy.org > http://galaxyproject.org > > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

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(no subject)
by sreenivas kurukuti 07 Apr '11

07 Apr '11

-- Sreenivasulu Kurukuti PhD Department of Animal Sciences School of Life Sciences University of Hyderabad Hyderabad-500 046 A.P., India

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BED to GFF
by Keith Giles 07 Apr '11

07 Apr '11

I am trying to use the galaxy "BED to GFF" function. The operation worked, but instead of giving me back any feature information (e.g., exon, intron, repeat, etc.); I just received back the sequence of the interval contained within the BED file. Does anyone know what I'm doing wrong? Moreover, does anyone know the best way to map each read of a RNAseq run to a given feature?

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