Re: [galaxy-user] can galaxy analyze SOLiD XSQ dataset except csfasta/qual data?
Hi Uma, If you look under 'NGS Mapping' there is 'Map with Bowtie for SOLiD' and 'Map with BWA for SOLiD' They take fastq, but you can use 'NGS: QC and manipulation' 'Convert' to generate a fastq file from fastqc and qual files. Or at least you could for SOLiD4 files. Ian From: galaxy-user-boun...@lists.bx.psu.edu [galaxy-user-boun...@lists.bx.psu.edu] on behalf of Chandran, Uma [chandra...@upmc.edu] Sent: 11 March 2014 13:14 To: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] can galaxy analyze SOLiD XSQ dataset except csfasta/qual data? Are there mappers for SoLiD 5500 on Galaxy? If so, do they take csfasta files as input? Thanks Uma Chandran ___ 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] Cuffdiff output
I am quite new to RNA-seq analysis, but what I have learned so far is that replicates are important. If you have this result with no replicates then P-values are more or less meaningless. You can also gauge what is happening by looking at the modelled read count output. If the counts are both less than 50ish you are unlikely to have a robust result for that gene/transcript. Ian From: galaxy-user-boun...@lists.bx.psu.edu [galaxy-user-boun...@lists.bx.psu.edu] on behalf of Malik, Shivani [shivani.ma...@ucsf.edu] Sent: 11 March 2014 21:43 To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] Cuffdiff output Hi, I have a question about interpreting the cuffdiff data and how to pick up significant genes. I have genes which show ~8 fold change between 2 conditions: eg from FPKM of 0.08 to 28 and yet they are not significant. Is there is threshold of FPKM below which Cuffdiff does not consider it an FPKM to be valid and hence significance in no? What downstream analysis should I use to extract a meaningful list of genes from the Cuffdiff data? Also, I filtered out FPKMs which were below 5 in both conditions? Is that reasonable? Thanks Shivani ___ 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/ ___ 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] Update from server failed several times
Hello, I deleted some files, because I reached 100% of the data volume I could use; my actual volume is 76 GB. I'm waiting now for an update from the server, that I reduced the data volume and can continue with my analysis. But I got a red note on the history for several times, that the update failed and that I should contact you, when it does so. What could I do now, to get an update from the server? Thanks in advance! Best, Meike ___ 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] Update from server failed several times
For all users: The tutorial on uploading data is incorrect. I do not think they have updated how to upload data yet. Scott Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core NextGen Sequencing/Flow Cytometry University of Vermont and Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2482 (AGTC) On 3/12/2014 11:58 AM, meike.l...@mdc-berlin.de wrote: Hello, I deleted some files, because I reached 100% of the data volume I could use; my actual volume is 76 GB. I'm waiting now for an update from the server, that I reduced the data volume and can continue with my analysis. But I got a red note on the history for several times, that the update failed and that I should contact you, when it does so. What could I do now, to get an update from the server? Thanks in advance! Best, Meike ___ 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/ ___ 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] File upload
Hi Scott, Is the 'Get Data - Upload File' tool no longer functioning for you? Can I help with using Main or is this on a local/cloud instance that needs to be set up? https://wiki.galaxyproject.org/Support#Loading_data It is correct that the addition upload methods via the Load Data process - found at the top of the tool panel - are not included in our tutorials/vidoes yet. This is very new set of methods (first was placed on Main at the end of January) and may still undergo some changes. We expect this to stabilize near-term and then be documented. Both tools will continue to co-exist. If there are any usage question right now (you or others) please let us know and we can help. The functions are either the same or very similar to the 'Upload File' tool, just presented in a different pop-up interface, plus now include convenience/feedback features. Thanks! Jen Galaxy team On 3/12/14 12:57 PM, Scott Tighe wrote: For all users: The tutorial on uploading data is incorrect. I do not think they have updated how to upload data yet. Scott Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core NextGen Sequencing/Flow Cytometry University of Vermont and Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2482 (AGTC) -- Jennifer Hillman-Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Update from server failed several times
Hi Meike, Our apologies for the server issues, these were transitory for a short window but should be fine now. The issue with history pane updates are unrelated to the deletion/purging of data. The expectation is that the database can take up to a few hours to update quota usage after permanently deleting/purging data - this is dependent on overall server load and often is much quicker. You hopefully have already seen this updated by now. The history pane display was the issue on our side. Help with deleting data is on this wiki, see section #8. Permanently deleting/purging data is the only way to impact quota usage. The Managing Histories video shows how to find data that is deleted, but not permanently deleted. https://wiki.galaxyproject.org/Learn/Managing%20Datasets http://vimeo.com/galaxyproject/managehistories Thanks! Jen Galaxy team On 3/12/14 11:58 AM, meike.l...@mdc-berlin.de wrote: Hello, I deleted some files, because I reached 100% of the data volume I could use; my actual volume is 76 GB. I'm waiting now for an update from the server, that I reduced the data volume and can continue with my analysis. But I got a red note on the history for several times, that the update failed and that I should contact you, when it does so. What could I do now, to get an update from the server? Thanks in advance! Best, Meike ___ 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/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] SnpEff on Main
Hi Sathya, The SnpEff tool is set up at this time for annotation with the /C. elegans/ WS220 genome only. Including human in the future on the public Main server at http://usegalaxy.org is under current evaluation. For now, use the tool in a local or cloud Galaxy instance, with the tool installed from the Tool Shed. Help to get started can be found here: http://getgalaxy.org http://usegalaxy.org/cloud http://usegalaxy.org/toolshed Take care, Jen Galaxy team On 3/12/14 1:44 AM, Sathya wrote: I am working on the project to predict SNP from NGS data. I have found SNP using SAM tools and GATK (used reference hg19). I would like to know effect of SNP using SNPeff in GALAXY. I have given SNP in vcf format. I could not change the genome option as human, it is set is C.elegans by default Please help me to solve this ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server atusegalaxy.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- With regards, Sathya.B ___ 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/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] File upload
Hi Scott, I am sorry that you have been having problems - and hope that I can help. I just tested FTP right now - and it is working for me. My guess is that the server name being entered is incorrect. You want this to be "usegalaxy.org" (not "usergalaxy.org") for the main public site (or be whatever the base url is for the other public servers, that are supporting FTP, you may be using). On any server, this is generally noted on the 'Upload File' tool itself, in the FTP section paragraph. This is the section for the public server: The window on this tool is only appropriate for two types of upload functions, either typing in text or entering a remote URL where data is available. This remote URL could be to a FTP server, but the process is different from loading local data (on your own computer) via FTP to the Galaxy server. The video (also linked from the wiki) for this tool demonstrates all four methods for loading data. The first method is a basic browser upload of a small file - which seems to be what you are asking about - how can I help more with this part? http://vimeo.com/galaxyproject/upload For deleting data, you can either delete individual datasets or complete histories. Which are you having trouble with? There are two videos on this wiki about datasets/histories, but it sounds like they are not covering the part you need to know. If you want to provide more details, I can try to help. https://wiki.galaxyproject.org/Learn/Managing%20Datasets The server has been problematic this week, due to circumstances out of our direct control, so if you had problems earlier, trying again is most likely a good first pass solution. You can follow our Twitter feed for updates about Main @galaxyproject - posted on our wiki here: https://wiki.galaxyproject.org/Galaxy%20on%20Twitter Usability matters, so helping you to get these operations working will probably help others as well. And I can add into our documentation what is unclear or missing. Plus most of our wiki is open - community members are encouraged to add new pages or comments to fill in/share help ideas. Thanks! Jen Galaxy team On 3/12/14 2:11 PM, Scott Tighe wrote: Jennifer It is a total mystery how to get data uploaded. Just like it is a total mystery how to delete it. Spent an hour and a half reviewing your tutorials and trying FTP. The FTP does not work anymore and if you put the term usergalaxy.org in to the FTP window, it does not like that. The tutorials were not useful and appear to be based on FTP. Maybe you could do a tutorial on how exactly to upload like 10gB. Arrggg Thanks Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core NextGen Sequencing/Flow Cytometry University of Vermont and Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2482 (AGTC) On 3/12/2014 1:17 PM, Jennifer Jackson wrote: Hi Scott, Is the 'Get Data - Upload File' tool no longer functioning for you? Can I help with using Main or is this on a local/cloud instance that needs to be set up? https://wiki.galaxyproject.org/Support#Loading_data It is correct that the addition upload methods via the "Load Data" process - found at the top of the tool panel - are not included in our tutorials/vidoes yet. This is very new set of methods (first was placed on Main at the end of January) and may still undergo some changes. We expect this to stabilize near-term and then be documented. Both tools will continue to co-exist. If there are any usage question right now (you or others) please let us know and we can help. The functions are either the same or very similar to the 'Upload File' tool, just presented in a different pop-up interface, plus now include convenience/feedback features. Thanks! Jen Galaxy team On 3/12/14 12:57 PM, Scott Tighe wrote: For all users: The tutorial on uploading data is incorrect. I do not think they have updated "how to upload data" yet. Scott Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core NextGen Sequencing/Flow Cytometry University of Vermont and Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2482 (AGTC) -- Jennifer
[galaxy-user] adding danrer7 as a reference genome for tophat2
Can you add danrer7 as a reference genome for tophat2 for online Galaxy? Its there for tophat for Illumina. Elwood Linney ___ 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] adding danrer7 as a reference genome for tophat2
Hello Dr. Linney, This genome (multiple releases, including danRer7) is scheduled for the next batch of genome processing. You will see the last two batches published to the public Main instance first - sometime next week - and this next batch update published around the start of April. (There may be other small data releases in between). So that you can follow progress, I added an annotation to the public Trello genome request ticket here. If the genome is published earlier than the other requests, any new tickets will be linked: https://trello.com/c/YqRsZnFI (Trello help - https://wiki.galaxyproject.org/Issues) A new wiki area is in progress that will outline our updated data release batch snapshot process - including the new contents of each snapshot. (A snapshot is a versioned data release). Each release, a tweet will go out to the @galaxyproject Twitter feed that includes a link to the wiki with details. If you don't use Twitter, the posts are also available here on our wiki: https://wiki.galaxyproject.org/Galaxy%20on%20Twitter Now is a good time to make requests - for you and others. After the update next week, please review (many genomes will be new have added content, please check first) and then make requests via Trello using this Inbox card for prioritization. Details matter. https://trello.com/c/mJWnAuuQ Thanks! Jen Galaxy team On 3/12/14 3:23 PM, Elwood Linney wrote: Can you add danrer7 as a reference genome for tophat2 for online Galaxy? Its there for tophat for Illumina. Elwood Linney ___ 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/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
