[galaxy-user] Make a vcf file
Hi, This may be a dense question, but how do we generate a vcf file from the public version of Galaxy? Am I missing something obvious? 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 ___ 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] filtering pile-up fails
Dear All, I have been successful by using the online tool to align Illumina pair end reads , each direction 5GB, and also generated a pileup of 680,000,000 lines, but the filtering of the pileup always fails, it runs for several hours and I get an empty file back. I tried different options and different pileups, always the same. Could somebody please help or what is the trick? Thank you Sebahattin ___ 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] Solution for: Error running cuffdiff. Error: cannot open reference GTF file CONDITION, CONTROL for reading
The problem ended being the use of Perform Bias Correction(-b) and a GTF file with no Database/Build associated. Looking at cuffdiff wrapper I found, if a FASTA reference is not selected from the history, the FASTA reference of the GTF file associated build is used. If there is not build association, your cuffdiff run will fail with this not so helpful error. My feeling is, cuffdiff should check for a non-dashed string after '-b' and complain if is absents, but this doesn't happen currently. Agreed. I implemented the spirit of this functionality via argument checking in galaxy-central changeset 71031bf3105c Best, J. ___ 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] Clustering with cuffcompare or cuffdiff results
Dear Sir or Madam, I am planning to do clustering of several libraries based on the output of cuffcompare or cuffdiff, as they allow me to construct a matrix whose columns represent the libraries and rows are the count of transcripts or genes. I want to construct the matrix because it is the required input format of many RNA-seq clustering softwares, e.g. baySeq, HTSCluster. However, by reading the answer of question I want to find differentially expressed genes. Can I use Cufflinks in conjunction with count-based differential expression packages? in the cufflinks FAQ list, it is suggested not to convert FPKM value to count data. Now my question is 1. It seems that it is better to run everything up to cuffdiff, but does cuffdiff allow multiple sample comparison because I read somewhere that even for multi-samples it still compare tham pairwisely? In a sense, because I want to do clustering which needs some quantitative data source to do the merging, will cuffdiff provide me some quantitative measures rather than the test score and p-value which is too qualitative to include? 2. If I really need to get count data from the FPKM values, how do I obtain the mentioned effective length? Would it be better if I treat each assembled transcript as an object in clustering, rather than genes. What does it mean you'd be throwing away Cufflinks' uncertainty even with using isoforms as objects? How should I include the uncertainty into my clustering? Best, Sherry ___ 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] Clustering with cuffcompare or cuffdiff results
1. It seems that it is better to run everything up to cuffdiff, but does cuffdiff allow multiple sample comparison because I read somewhere that even for multi-samples it still compare tham pairwisely? Cuffdiff supports replicate analysis. In a sense, because I want to do clustering which needs some quantitative data source to do the merging, will cuffdiff provide me some quantitative measures rather than the test score and p-value which is too qualitative to include? Take a look at the Cuffdiff documentation for outputs: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff_output 2. If I really need to get count data from the FPKM values, how do I obtain the mentioned effective length? Would it be better if I treat each assembled transcript as an object in clustering, rather than genes. What does it mean you'd be throwing away Cufflinks' uncertainty even with using isoforms as objects? How should I include the uncertainty into my clustering? These FAQs from http://cufflinks.cbcb.umd.edu/faq.html address your questions: -- I want to find differentially expressed genes. Can I use Cufflinks in conjunction with count-based differential expression packages? It's possible, but we strongly advise against this. Current count-based differential expression tools are poorly suited to differential expression analysis in genomes with alternatively spliced genes. The main reason for this is that when a gene has multiple isoforms, a change in the total number of reads or fragments from that gene doesn't always correspond to a change in expression for that gene. Conversely, a gene's expression may change, but the total number of fragments generated by its isoforms may be very similar. In order to detect changes accurately, it's necessary to estimate how many fragments came from each individual splice variant in each sample. Current count-based tools don't do this (to our knowledge - please send us email if you know of one!). Even if they did, fragments that come from parts of genes that are shared by more than one splice variant can't generally assigned to a single isoform, so the fragment counts for each isoform are only estimates, and there is some uncertainty in the counts. Isoforms that are very similar will have a great deal of uncertainty surrounding their fragment counts. This uncertainty needs to be accounted for when testing for differential expression. So while you could use Cufflinks to estimate isoform-level counts, you'd be throwing away Cufflinks' uncertainty, and thus have more confidence in the differences you see than you really should. This will probably lead to many false positives in your analysis. Furthermore, we do not normalize simply by the length to calculate FPKM but an effective length, as explained in our publications. Calculting counts from FPKM by multiplying by the length will give incorrect results. We strongly encourage you to consider using Cuffdiff to find differentially expressed genes and transcripts. Will you please report how many fragments come from each transcript in a future release? For the foreseeable future, we will not be reporting the number of fragments we think originated from each transcript. People who have asked for this almost always want to use Cufflinks in conjunction with count-based differential expression packages, which is not a good idea. We're trying to keep our output formats as simple as possible. -- Best, J. ___ 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] filtering pile-up fails
Hello Sebahattin, It may be that the data is too large to run on the Galaxy public instance, which means that a local or cloud instance would be the next recommendation, as explained in this wiki: http://wiki.g2.bx.psu.edu/Big%20Picture/Choices But, before you make the investment of moving you analysis, I'd like to offer to double check to see if there are any tool use modifications that will allow the job to process given the resources available on Main. What I will need is for you to send in a tool error report by clicking on the green bug icon in the red error dataset. Please include this email address in the comments if it is not the one you also use with your galaxy account, so that I can link the two questions. If the tool just gave an empty set, but not an actual error, then use Options - Share or Publish, generate the share link, copy that and email it back to me directly. Please note the problem datasets if not obvious and leave all inputs and errors in an undeleted state (please undelete if necessary) so that I can examine the entire data path that lead up to the error. If you want to try to troubleshoot on your own as well, some general advice is in this part of the Support wiki: http://wiki.g2.bx.psu.edu/Support#Error_from_tools Hopefully we can work out a solution, Best, Jen Galaxy team On 2/14/12 4:11 AM, Sebahattin Cirak wrote: Dear All, I have been successful by using the online tool to align Illumina pair end reads , each direction 5GB, and also generated a pileup of 680,000,000 lines, but the filtering of the pileup always fails, it runs for several hours and I get an empty file back. I tried different options and different pileups, always the same. Could somebody please help or what is the trick? Thank you Sebahattin ___ 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://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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] bug for mate pairs colorspace to sequence conversion
Hi Philipp, Sorry for the delay in reply, the question is a bit confusing since the conversion tools allow for the adapter base to be specified (and the default is a G). I am not sure we are talking about the same tool, so to clear things up, would you please send a shared history link and any other details that you think will help, and then I'll try to provide some more feedback? Including opening an enhancement request ticket if that seems appropriate after we discuss the data tools. To share, use Options - Share or Publish, generate the share link, copy that, and email it directly back to me (not the entire list). Make certain that all input are present and any attempted tool runs, successful or failure are present and undeleted. Please note the exact tools that you want to use, including the settings you think are the best fit, and what you think is missing, the more detail the better. Thank you and I will watch for your reply, Best, Jen Galaxy team On 2/2/12 9:41 AM, philipp.bernin...@unibas.ch wrote: Hi, I have a problem converting paired reads with paired end reads from ABi, in the color code the reads started with a G and afterwards with numbers instead of T02102103... , so I guess the program assumes the T as hardcoded instead of using the G as last base best Philipp This message was sent using IMP, the Internet Messaging Program. ___ 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://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
