[galaxy-user] Text Manipulation: Filter out duplicates (uniq) from an plain text file ?
Hey galaxy users, Thats a fairly good question from one of my colleagues. I've looked through the menus (mainly Text Manipulation and Filter and Sort(Select)), googled (on the mailing list archives too), but couldn't find an answer: How should I remove duplicates on plain text files without resorting to: echo file|sort|uniq before uploading the file/text. or Putting a regexp together to replace the duplicate occurences as in: http://www.regular-expressions.info/duplicatelines.html I'm pretty sure I'm missing some really basic stuff here... is this basic operation something supposed to be done outside galaxy perhaps ? Thanks in advance ! ___ 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] Text Manipulation: Filter out duplicates (uniq) from an plain text file ?
On Fri, May 6, 2011 at 3:16 PM, Roman Valls brainst...@nopcode.org wrote: Well, having similarly basic tools (in Galaxy) that can be performed on the commandline, such as sort or cut I just wondered how come a uniq is not there on the tool panel in some form/name. Thanks for the feedback Rory ! That's a timely question - I was also looking for something within Galaxy to take a text file and remove duplicate lines. Peter ___ 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] Text Manipulation: Filter out duplicates (uniq) from an plain text file ?
Hi Peter and Roman, The Count tool under Statistics section provides uniq-like functionality. If you run this tool by selecting all columns under Count occurrences of values in column(s) field, your output will contain one line per record, with the 1st column containing the number of occurrences of each record. Hope this answers your question. Thanks for using Galaxy, Guru. On Fri, May 6, 2011 at 10:22 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Fri, May 6, 2011 at 3:16 PM, Roman Valls brainst...@nopcode.org wrote: Well, having similarly basic tools (in Galaxy) that can be performed on the commandline, such as sort or cut I just wondered how come a uniq is not there on the tool panel in some form/name. Thanks for the feedback Rory ! That's a timely question - I was also looking for something within Galaxy to take a text file and remove duplicate lines. Peter ___ 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/ -- Graduate student, Bioinformatics and Genomics Makova lab/Galaxy team Penn State University 505 Wartik lab University Park PA 16802 g...@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] RNA seq analysis
Hi I have a couple of questions regarding RNA seq analysis. My questions are 1.I need to use a viral genome (very small, ~2kb ) as a reference genome and it is not available in Galaxy. I guess I can use this data from my history. I have a fasta file but I am not sure whether I have to do some kind of indexing or not. 2. In Tophat, default for maximum number of alignments to be allowed is 40. What my understanding is a single read can be aligned maximum 40 different places. I am wondering why this is 40. Is there any specific reason? If I need unique mapping, I have to use 1 instead of 40. Am I correct? Thanks SP ___ 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] RNA seq analysis
Hi, I have done exactly the same kind of thing for adenovirus so I can help with it. In answer to question 1 you do not need to index it will be done for you when tophat is called. Secondly you should leave the 40 multihits as it is and post analysis filter out the multihits - this will allow you to determine if you do have a multihit problem or not and if so whether it is a big problem and where it is on the genome. I have a workflow on Galaxy which you can use called Bristol workflow to get sorted unique proper pair mapped reads. If you plug in your sam file it should give you files listing only unique hits and those which map more than once. This workflow assumes you have paired end data but it can be modified to work with single end reads as well. Hope this helps. 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 6 May 2011, at 17:09, puvan...@umn.edu wrote: Hi I have a couple of questions regarding RNA seq analysis. My questions are 1.I need to use a viral genome (very small, ~2kb ) as a reference genome and it is not available in Galaxy. I guess I can use this data from my history. I have a fasta file but I am not sure whether I have to do some kind of indexing or not. 2. In Tophat, default for maximum number of alignments to be allowed is 40. What my understanding is a single read can be aligned maximum 40 different places. I am wondering why this is 40. Is there any specific reason? If I need unique mapping, I have to use 1 instead of 40. Am I correct? Thanks SP ___ 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] RNA seq analysis
Hi David, Thanks!When I tried to run Tophat, it doesn't recognise my FASTA file and it says History does not include a dataset of the required format / build. Do you have any thoughts about this? Now it makes more sense about multihits. Thanks for sharing your workflow. With regards Sumathy On May 6 2011, David Matthews wrote: Hi, I have done exactly the same kind of thing for adenovirus so I can help with it. In answer to question 1 you do not need to index it will be done for you when tophat is called. Secondly you should leave the 40 multihits as it is and post analysis filter out the multihits - this will allow you to determine if you do have a multihit problem or not and if so whether it is a big problem and where it is on the genome. I have a workflow on Galaxy which you can use called Bristol workflow to get sorted unique proper pair mapped reads. If you plug in your sam file it should give you files listing only unique hits and those which map more than once. This workflow assumes you have paired end data but it can be modified to work with single end reads as well. Hope this helps. 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 6 May 2011, at 17:09, puvan...@umn.edu wrote: Hi I have a couple of questions regarding RNA seq analysis. My questions are 1.I need to use a viral genome (very small, ~2kb ) as a reference genome and it is not available in Galaxy. I guess I can use this data from my history. I have a fasta file but I am not sure whether I have to do some kind of indexing or not. 2. In Tophat, default for maximum number of alignments to be allowed is 40. What my understanding is a single read can be aligned maximum 40 different places. I am wondering why this is 40. Is there any specific reason? If I need unique mapping, I have to use 1 instead of 40. Am I correct? Thanks SP ___ 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/ -- Sumathy Puvanendiran Graduate student ___ 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] RNA seq analysis
Hi, You need to run fastq groomer on your rna-seq data. Your reference is fine as a fasta. Austin On Fri, May 6, 2011 at 10:26 AM, puvan...@umn.edu wrote: Hi David, Thanks!When I tried to run Tophat, it doesn't recognise my FASTA file and it says History does not include a dataset of the required format / build. Do you have any thoughts about this? Now it makes more sense about multihits. Thanks for sharing your workflow. With regards Sumathy On May 6 2011, David Matthews wrote: Hi, I have done exactly the same kind of thing for adenovirus so I can help with it. In answer to question 1 you do not need to index it will be done for you when tophat is called. Secondly you should leave the 40 multihits as it is and post analysis filter out the multihits - this will allow you to determine if you do have a multihit problem or not and if so whether it is a big problem and where it is on the genome. I have a workflow on Galaxy which you can use called Bristol workflow to get sorted unique proper pair mapped reads. If you plug in your sam file it should give you files listing only unique hits and those which map more than once. This workflow assumes you have paired end data but it can be modified to work with single end reads as well. Hope this helps. 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 6 May 2011, at 17:09, puvan...@umn.edu wrote: Hi I have a couple of questions regarding RNA seq analysis. My questions are 1.I need to use a viral genome (very small, ~2kb ) as a reference genome and it is not available in Galaxy. I guess I can use this data from my history. I have a fasta file but I am not sure whether I have to do some kind of indexing or not. 2. In Tophat, default for maximum number of alignments to be allowed is 40. What my understanding is a single read can be aligned maximum 40 different places. I am wondering why this is 40. Is there any specific reason? If I need unique mapping, I have to use 1 instead of 40. Am I correct? Thanks SP ___ 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/ -- Sumathy Puvanendiran Graduate student ___ 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] RNA seq analysis
Hi Austin I did all these (grooming and trimming)on rna-seq data and I don't have a problem with built in genome . I'll try again! Thanks Sumathy On May 6 2011, Austin Paul wrote: Hi, You need to run fastq groomer on your rna-seq data. Your reference is fine as a fasta. Austin On Fri, May 6, 2011 at 10:26 AM, puvan...@umn.edu wrote: Hi David, Thanks!When I tried to run Tophat, it doesn't recognise my FASTA file and it says History does not include a dataset of the required format / build. Do you have any thoughts about this? Now it makes more sense about multihits. Thanks for sharing your workflow. With regards Sumathy On May 6 2011, David Matthews wrote: Hi, I have done exactly the same kind of thing for adenovirus so I can help with it. In answer to question 1 you do not need to index it will be done for you when tophat is called. Secondly you should leave the 40 multihits as it is and post analysis filter out the multihits - this will allow you to determine if you do have a multihit problem or not and if so whether it is a big problem and where it is on the genome. I have a workflow on Galaxy which you can use called Bristol workflow to get sorted unique proper pair mapped reads. If you plug in your sam file it should give you files listing only unique hits and those which map more than once. This workflow assumes you have paired end data but it can be modified to work with single end reads as well. Hope this helps. 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 6 May 2011, at 17:09, puvan...@umn.edu wrote: Hi I have a couple of questions regarding RNA seq analysis. My questions are 1.I need to use a viral genome (very small, ~2kb ) as a reference genome and it is not available in Galaxy. I guess I can use this data from my history. I have a fasta file but I am not sure whether I have to do some kind of indexing or not. 2. In Tophat, default for maximum number of alignments to be allowed is 40. What my understanding is a single read can be aligned maximum 40 different places. I am wondering why this is 40. Is there any specific reason? If I need unique mapping, I have to use 1 instead of 40. Am I correct? Thanks SP ___ 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/ -- Sumathy Puvanendiran Graduate student ___ 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/ -- Sumathy Puvanendiran Graduate student ___ 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] Composite Datatypes Q.
I have a program I'm trying to galaxify that emits a variable number of result files. I would like the output of my Galaxy tool to show up in Galaxy as an html file with links to the result files. So when you click on the eye, the html file should up in the middle pane ... sorry if I'm not describing this in an elegant way. Creating a composite datatype is the way to go in this situation, correct? I'm creating a class that inherits from Html. How do I get the result returned from my custom generate_primary_file function to show up as a tool's output ... if that's the right way to go about this? 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/
[galaxy-user] Megblast GIs
We have a local install of Galaxy and are using it for training grad and undergrad students (using the Windshield Splatter data). We have a relatively new install and the Megablast seems to be doing something funny with the output in that column 2 which is supposed to be the GI of the database hit is now two numbers joined with an underline (see below). I need to tell my IT people what is wrong so they can correct the problem. BL1-1-3 157649053_11175091.30 46 4 0 10 55 58541 58496 2e- 06 60.0 BL1-1-5 161788633_175843100.00 26 0 0 15 40 48812 48787 4e- 04 52.0 -- Douglas Rhoads, Professor of Biological Sciences Director of Graduate Program in Cell and Molecular Biology 601 SCEN, Dept. of Biological Sciences, 1 University of Arkansas, Fayetteville, AR 72701-1201 drhoads(at)uark.edu, http://www.uark.edu/ua/drhoads phone: 479-575-3251 FAX: 479-575-4010 ___ 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] RNA seq analysis
There are many ways. I typically use IGV. It needs a sam file, so I first convert the bam to sam in galaxy, then download the sam file. In IGV, I upload the reference and the sam file, then use IGVtools to index the sam file, then I can visualize the data. Austin On Fri, May 6, 2011 at 5:30 PM, puvan...@umn.edu wrote: Hello I was able to run RNA seq data against a custom build genome. How can I visualize the results. I tried via trackster and unfortunately I couldn't. Can you help me? Thanks Sumathy ___ 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] RNA seq analysis
Oops. Good to know. Thanks. Austin On Fri, May 6, 2011 at 6:02 PM, Sean Davis sdav...@mail.nih.gov wrote: IGV reads BAM files just fine; no need to convert to SAM. Sean On Fri, May 6, 2011 at 8:45 PM, Austin Paul austi...@usc.edu wrote: There are many ways. I typically use IGV. It needs a sam file, so I first convert the bam to sam in galaxy, then download the sam file. In IGV, I upload the reference and the sam file, then use IGVtools to index the sam file, then I can visualize the data. Austin On Fri, May 6, 2011 at 5:30 PM, puvan...@umn.edu wrote: Hello I was able to run RNA seq data against a custom build genome. How can I visualize the results. I tried via trackster and unfortunately I couldn't. Can you help me? Thanks Sumathy ___ 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] RNA seq analysis
Hi Vasu, I'm going to add the function to index BAM files soon, using Picard. In the beginning there was no java BAM reader, only SAM, and I added the index then. Indexed BAMs came along later, but that's probably more than you want to know...I think most people will still use Galaxy to index as it can take a long time, but I agree with you on the convenience factor. Jim On May 6, 2011, at 9:36 PM, vasu punj wrote: One of the problem is IGV dont have option of creating index file so one has to create index file in Galaxy first to view in IGV. Jim I have been using IGV 2 beta version it is great work but How hard is to include index functionality with in IGV. I know we can use sam tools also but just for convinence if it is not that much of work. Vasu --- On Fri, 5/6/11, Sean Davis ssdav...@mail.nih.gov wrote: From: Sean Davis sdav...@mail.nih.gov Subject: Re: [galaxy-user] RNA seq analysis To: Austin Paul austi...@usc.edu Cc: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu, puvan...@umn.edu puvan...@umn.edu Date: Friday, May 6, 2011, 8:02 PM IGV reads BAM files just fine; no need to convert to SAM. Sean On Fri, May 6, 2011 at 8:45 PM, Austin Paul austi...@usc.edu wrote: There are many ways. I typically use IGV. It needs a sam file, so I first convert the bam to sam in galaxy, then download the sam file. In IGV, I upload the reference and the sam file, then use IGVtools to index the sam file, then I can visualize the data. Austin On Fri, May 6, 2011 at 5:30 PM, puvan...@umn.edu wrote: Hello I was able to run RNA seq data against a custom build genome. How can I visualize the results. I tried via trackster and unfortunately I couldn't. Can you help me? Thanks Sumathy ___ 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/ -Inline Attachment Follows- ___ 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/
Re: [galaxy-user] RNA seq analysis
Hi I may be doing in a wrong way. I clicked trackster and I added the custom build genome. Since it is a very small genome (~2kb), I considered this as a single contig. Then I cliked add tracks and added my data file. But I got a message no data for this contig. Whenever I used built in genomes I did not have any problem. I guess I am doing something wrong here. Sumathy On May 6 2011, Jeremy Goecks wrote: Sumathy, What kind of problems are you having with Trackster? J. On May 6, 2011, at 8:30 PM, puvan...@umn.edu wrote: Hello I was able to run RNA seq data against a custom build genome. How can I visualize the results. I tried via trackster and unfortunately I couldn't. Can you help me? Thanks Sumathy ___ 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/ -- Sumathy Puvanendiran Graduate student ___ 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] RNA seq analysis
Thanks Jim, Vasu --- On Fri, 5/6/11, Jim Robinson jrobi...@broadinstitute.org wrote: From: Jim Robinson jrobi...@broadinstitute.org Subject: Re: [galaxy-user] RNA seq analysis To: vasu punj pu...@yahoo.com Cc: Austin Paul austi...@usc.edu, Sean Davis sdav...@mail.nih.gov, galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu, puvan...@umn.edu puvan...@umn.edu Date: Friday, May 6, 2011, 9:01 PM Hi Vasu, I'm going to add the function to index BAM files soon, using Picard. In the beginning there was no java BAM reader, only SAM, and I added the index then. Indexed BAMs came along later, but that's probably more than you want to know... I think most people will still use Galaxy to index as it can take a long time, but I agree with you on the convenience factor. Jim On May 6, 2011, at 9:36 PM, vasu punj wrote: One of the problem is IGV dont have option of creating index file so one has to create index file in Galaxy first to view in IGV. Jim I have been using IGV 2 beta version it is great work but How hard is to include index functionality with in IGV. I know we can use sam tools also but just for convinence if it is not that much of work. Vasu --- On Fri, 5/6/11, Sean Davis ssdav...@mail.nih.gov wrote: From: Sean Davis sdav...@mail.nih.gov Subject: Re: [galaxy-user] RNA seq analysis To: Austin Paul austi...@usc.edu Cc: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu, puvan...@umn.edu puvan...@umn.edu Date: Friday, May 6, 2011, 8:02 PM IGV reads BAM files just fine; no need to convert to SAM. Sean On Fri, May 6, 2011 at 8:45 PM, Austin Paul austi...@usc.edu wrote: There are many ways. I typically use IGV. It needs a sam file, so I first convert the bam to sam in galaxy, then download the sam file. In IGV, I upload the reference and the sam file, then use IGVtools to index the sam file, then I can visualize the data. Austin On Fri, May 6, 2011 at 5:30 PM, puvan...@umn.edu wrote: Hello I was able to run RNA seq data against a custom build genome. How can I visualize the results. I tried via trackster and unfortunately I couldn't. Can you help me? Thanks Sumathy ___ 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/ -Inline Attachment Follows- ___ 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/
