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from Bowtie mapping to gene names
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from Bowtie mapping to gene names
 
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Hi,
I have reads from Illumina paired-end run mapped against reference genome using Bowtie. Is there a Galaxy tool which would allow me to extract gene names from the mapped chromosomal regions? In this case I have cat genome, example of the output row is bellow. Thanks for anymhelp, Daniel HWUSI-EAS610_110227_00028:5:1:7767:999#0 99 chrE2 27900093 255 82M = 27900139 128 NACCTGTTATGTACTAAGAAGCTTATTCTCCCANNNNNNCTNNNNNNNNNCATATGTNGNGNNNNNNNNNNNNNNNNNNNAA ################################################################################## XA:i:2 MD:Z:0A17T14T0G0C0T0G0A2C0A0T0C0A0A0A0G0G7G1T1A0C0C0C0C0T0T0A0G0T0G0C0C0C0G0T0G0A0T2 NM:i:38 ------------------------------------------------ Daniel Elleder, Ph.D. Postdoctoral fellow Center for Infectious Disease Dynamics Pennsylvania State University 613 Mueller Laboratory University Park, PA 16802 tel: (814) 867-2122 ___________________________________________________________ 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: from Bowtie mapping to gene names
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Daniel:
To get a good idea on how Galaxy handles so called interval operations take a look at http://usegalaxy.org/galaxy101. The answer to your question depends on what you would like to do. Are interested in obtaining the read coverage for a set of genes or simply identifying a set of reads mapping to a set of genes? Thanks, anton On Apr 11, 2011, at 11:17 AM, Daniel Elleder wrote: > Hi, > > I have reads from Illumina paired-end run mapped against reference genome using Bowtie. Is there a Galaxy tool which would allow me to extract gene names from the mapped chromosomal regions? In this case I have cat genome, example of the output row is bellow. > > Thanks for anymhelp, > Daniel > > HWUSI-EAS610_110227_00028:5:1:7767:999#0 99 chrE2 27900093 255 82M = 27900139 > 128 > NACCTGTTATGTACTAAGAAGCTTATTCTCCCANNNNNNCTNNNNNNNNNCATATGTNGNGNNNNNNNNNNNNNNNNNNNAA ################################################################################## XA:i:2 MD:Z:0A17T14T0G0C0T0G0A2C0A0T0C0A0A0A0G0G7G1T1A0C0C0C0C0T0T0A0G0T0G0C0C0C0G0T0G0A0T2 NM:i:38 > > > ------------------------------------------------ > > Daniel Elleder, Ph.D. > Postdoctoral fellow > Center for Infectious Disease Dynamics > Pennsylvania State University > 613 Mueller Laboratory > University Park, PA 16802 > tel: (814) 867-2122 > > > ___________________________________________________________ > 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 ___________________________________________________________ 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: Help!!!!!! with Galaxy Cloud!!!!!
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___________________________________________________________ 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: Help!!!!!! with Galaxy Cloud!!!!!
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Hi Mike,
Try accessing your Galaxy instance now. It should be ok. The link in your email contained the IP for your instance so I took the liberty of restarting Galaxy and that brought it back up. There seems to have been an issue with Galaxy accessing its database and that resulted in Galaxy crashing. We'll look into why that happened in the first place but should be ok now.
Let me know if you have any more trouble, Enis
On Tue, Apr 12, 2011 at 2:49 PM, Mike Dufault <[hidden email]> wrote:
___________________________________________________________ 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: Help!!!!!! with Galaxy Cloud!!!!!
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___________________________________________________________ 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: Help!!!!!! with Galaxy Cloud!!!!!
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Ahh, for some reason cloudman is thinking Galaxy is not 'running' but still 'starting' and has thus not enabled the given button. To access the analysis, in your browser, just delete the '/cloud' part of the URL and that should load Galaxy.
Sorry about the confusion, Enis
On Tue, Apr 12, 2011 at 9:12 PM, Mike Dufault <[hidden email]> wrote:
___________________________________________________________ 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: Help!!!!!! with Galaxy Cloud!!!!!
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___________________________________________________________ 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: Help!!!!!! with Galaxy Cloud!!!!!
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Galaxy has the functionality to recover any jobs that were running after it's restarted so it is quite possible to for the job to still be running. In addition, from the cloudman console, it appears that at least one instance is pretty heavily loaded so that can also mean that the job is still running. However, without actually accessing the instance through the command line and checking the status of the job queue, it is not possible to tell if the job is - actually running. Do you know how to do that? It's just a few commands in the terminal:
- access the instance [local]$ ssh -i <path to the private key you downloaded from AWS when you created a key pair> ubuntu@<instance public DNS> - become galaxy user [ec2]$ sudo su galaxy
- list any running jobs [ec2]$ qstat If that command returns a list of jobs and the jobs are in stare 'r' (running), the job is still running; otherwise, no. Let me know how it goes, Enis On Tue, Apr 12, 2011 at 9:49 PM, Mike Dufault <[hidden email]> wrote:
___________________________________________________________ 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/ |
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___________________________________________________________ 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: Help!!!!!! with Galaxy Cloud!!!!!
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Hi Vasu,
I am not sure I understand your question but the general instructions on how to get started and use Galaxy on the cloud (i.e., Cloudman) are available at usegalaxy.org/cloud
Let us know if you that page does not answer your questions, Enis
On Wed, Apr 13, 2011 at 9:40 AM, vasu punj <[hidden email]> wrote:
___________________________________________________________ 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: Help!!!!!! with Galaxy Cloud!!!!!
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___________________________________________________________ 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: Help!!!!!! with Galaxy Cloud!!!!!
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Hi Mike,
Once the given EBS volume is attached and mounted, all of the data should be in /mnt/galaxyData/files/000/ This assumes the file system is mounted to /mnt/galaxyData, which is where it would get mounted to automatically by cloudman on cluster instantiation.
Enis
On Wed, Apr 13, 2011 at 9:00 PM, Mike Dufault <[hidden email]> wrote:
___________________________________________________________ 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: Help!!!!!! with Galaxy Cloud!!!!!
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___________________________________________________________ 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: Help!!!!!! with Galaxy Cloud!!!!!
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Hi Mike,
You should be able to download the desired file(s) directly from Galaxy by expanding the desired history item and then clicking the 'disk' (i.e., download) icon. Alternatively, if you want to copy the file by hand directly from the file system on the instance, the following is the command to execute (note that the command is executed from your local machine):
scp -i <path to your AWS key pair file> ubuntu@<instance public DNS>:/mnt/galaxyData/files/000/<file name> . (also, note the '.' at the end of the command) This command will copy the remote file to your local machine and it will put it in your current directory.
Once downloaded, the file can probably be opened with any text editor (unless it's a binary file, in which case it will have to be opened with the appropriate tool that can read the given file format).
Enis
On Fri, Apr 15, 2011 at 12:32 AM, Mike Dufault <[hidden email]> wrote:
___________________________________________________________ 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: Help!!!!!! with Galaxy Cloud!!!!!
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___________________________________________________________ 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: Help!!!!!! with Galaxy Cloud!!!!!
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I don't think you'll need to convert the file other than maybe renaming the extension (mv <filename>.dat filename.bam>) because Galaxy just adds that same extension to each file while the metadata that it keeps tell it which format the file is in. Just try opening the file up using the tool you were planning to use and it should work.
Enis
On Fri, Apr 15, 2011 at 8:49 AM, Mike Dufault <[hidden email]> wrote:
___________________________________________________________ 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/ |
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