Re: [galaxy-user] Variant annotation in galaxy
Hi Jen, thanks for your answer! Unfortunatelly I cannot run Galaxy locally (in my Institute we only have Windows computers), but I can try on a cloud. I have a DIAG account, do you know if Galaxy works there? Debora ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Concatenate variants from vcf files
Hello, is there a tool in the main Galaxy to extract a fasta alignment of my detected variants from a vcf file? I have 19 samples (plus the reference). Thanks! Debora ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Variant annotation in galaxy
Hallo Galaxy users, I would like to annotate variants (in vcf file) found in my bacterial genomes and look which of them cause non-synonymous mutations. I have found two tools in the Main Galaxy that I can use for this purpose (snpEff and Annovar), but I have problems with them. How can I change the input genome in snpEff? The only available choice in C. elegans. How can I choose my genome, already uploaded in my history? Regarding Annovar, which file formats are required as Gene annotations/ Annotation Regions/ Annotation Databases? Reading the tool manual, it seems I can create my own txt/tabular files and use them for annotation, but the tool in Galaxy doesn't allow me to select any file, even if I have txt files in my history. Any other suggested tool I can use? Thanks! Debora ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Read simulator
Dear all, I would like to perforn my SNP calling pipeline (for MySeq Illumina reads) to previously sequenced and assembled genomes. Is there any read simulator in the Main Galaxy? I am looking for something like the wgsim algorithm in SAMtools... Thanks! Debora ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Workflow does not run
Hello! I have a question about a workflow I have created from my history. I can edit and view it, but when I try to run it, a white page appears and I cannot do anything. I have created other worflows which perfectly run, but I don't know why this one doesn't. It includes 4 steps for GATK pre-processing steps (Indel Realigner, Count Covariates and Table Recalibration). What can the problem be? I would appreciate any input! Thanks Debora ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] SNP calling problems (Jennifer Jackson)
Hi Jen, thank you for your answer! I have used the Add or Replace group tool and it worked pretty well, so that I could use the FreeBayes tool with no problem! Now I have another question: I have been pre-processing my data with the NGS: GATK tools according to their Best Practices and I am ready for SNP calling. I have read the Unified Genotyper documentation and, since I am working with bacterial genome sequences, I would need to set the -sample-ploidy argument to 1 (default 2). I cannot find this option in the Galaxy version of this tool, not even in the advanced options. How can I do that? Thank you very much! Debora Message: 3 Date: Fri, 27 Sep 2013 14:02:50 -0700 From: Jennifer Jackson j...@bx.psu.edu To: garzetti garze...@mvp.uni-muenchen.de Cc: galaxy-u...@bx.psu.edu Subject: Re: [galaxy-user] SNP calling problems Message-ID: 5245f27a.7020...@bx.psu.edu Content-Type: text/plain; charset=iso-8859-1; Format=flowed Hi Debora, Sorry to hear that you are having problems. We can help get you going again! Please see below: On 9/26/13 7:20 AM, garzetti wrote: Dear all, I have been looking for an answer to my problem in all the Galaxy Support resources but with no success. I am sorry if this topic has been already discussed! So, I am analyzing MiSeq data on the main Galaxy. I have Fastq files from 4 paired-end samples. After having checked the quality with FastQC and groomed them, I have performed a BWA mapping, filtered the results and converted the SAM to BAM files (for each sample separately). I have then called SNPs with Freebayes and SAMtools, encountering problems in both cases. 1) SAMtools: if I run the Generate pileup tool, then the Filter pileup doesn't recognize any valid format in the files I have in my History and I cannot go on with the analysis. Why is that? What can I do? Make sure that the output format is set as pileup and the tool will accept the input. Click on the pencil icon to make the datatype assignment change. http://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset Note that Mpileup has an option to produce .bcf format, and that is not the same as pileup. If you have selected that type of output, then either re-run the tool with options that create pileup format, or convert bcf - vcf and use one of the tools that work with vcf format to work with your data downstream from there. 2) I have performed variant calling with Freebayes on single BAM files and on one merged BAM files from all my four BWA mapping files. In all cases, the last column is unknown, while it should be the name of my sample. This is not a big deal for the single vcf files, but from the merged BAM file, I cannot discriminate from which sample the SNPs were detected. I think there is a problem in the BAM files which are not properly indexed. Also Freebayes needs an RG tag. Is there a tool in Galaxy I can use to index BAM files, adding the RG tag? The tool NGS: Picard (beta) - Add or Replace Groups can be used to annotate SAM/BAM files. This tool can be a bit picky about formats, so just watch for that if you get an error. /_Quick tip:_/ You can click on the bug icon on failed datasets to see the complete error message and it will often tell you exactly what is wrong so that you can correct it (this doesn't automatically submit a bug, which is good to know when you are in a hurry at night or on weekends or just want to troubleshoot yourself). You can use this on any error dataset to get more information if the dataset's i info button's stderr/stdout links or attributes Info field does not provide enough details. = This functions on servers that have bug reporting enabled (the public Main server does, and this is straightforward to configure on local/cloud instances, including your own, even if you use one for small local file manipulations or file backup/storage (very handy key file backups are always a good idea, when doing analysis in general, anywhere). See the Admin wiki section for more. Going forward, there is a short screencast about the Learning resources in Galaxy here in a Page. It will be uploaded to Vimeo sometime in the next 24 hrs, and will be likely updated to include the very latest as the infrastructure updates on Main settle out in the next weeks or so, but for now here is the link: Click on the Learning Resources graphic to launch the quick tour: https://main.g2.bx.psu.edu/u/galaxyproject/p/screencasts-usegalaxyorg Galaxy team's Vimeo account: http://vimeo.com/channels/581769 We are uploading all of our vids, old new, right now and over next few days. We really like and hope our user's do too and follow along. The public Main server will have direct links to this content, in the center home page, soon as part of the New Improved Galaxy experience! I won't give an ETA, as this is in progress, but can hint that soon == expected very soon. (!) Good luck and let us know if you need more
[galaxy-user] SNP calling problems
Dear all, I have been looking for an answer to my problem in all the Galaxy Support resources but with no success. I am sorry if this topic has been already discussed! So, I am analyzing MiSeq data on the main Galaxy. I have Fastq files from 4 paired-end samples. After having checked the quality with FastQC and groomed them, I have performed a BWA mapping, filtered the results and converted the SAM to BAM files (for each sample separately). I have then called SNPs with Freebayes and SAMtools, encountering problems in both cases. 1) SAMtools: if I run the Generate pileup tool, then the Filter pileup doesn't recognize any valid format in the files I have in my History and I cannot go on with the analysis. Why is that? What can I do? 2) I have performed variant calling with Freebayes on single BAM files and on one merged BAM files from all my four BWA mapping files. In all cases, the last column is unknown, while it should be the name of my sample. This is not a big deal for the single vcf files, but from the merged BAM file, I cannot discriminate from which sample the SNPs were detected. I think there is a problem in the BAM files which are not properly indexed. Also Freebayes needs an RG tag. Is there a tool in Galaxy I can use to index BAM files, adding the RG tag? I hope someone can help me! Thank you very much! Debora -- Debora Garzetti, PhD Student AG Rakin Max von Pettenkofer-Institute, LMU Pettenkoferstraße 9A 80336 Munich E-mail: garze...@mvp.uni-muenchen.de Phone: +49 (0)89 2180 72915 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/