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SNP and INDEL detection
by Gabriela Ronquillo-Lopez 11 Oct '11

11 Oct '11

Hello, I am new using Galaxy, I would like ask if it is possible to perform a SNP and INDEL analysis between two SAM files (mutant and wt) with Galaxy. If so, could anyone give a hint in how to proceed? Many thanks for your help in advance, Kind regards, Maria G.

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Re: [galaxy-user] Q about 'Compute' tool
by Russell Bell 11 Oct '11

11 Oct '11

Ian, using your chr1 500 1000 geneA . + chr1 2000 2500 geneB . - problem i was able to get chr1 500 1000 geneA . + 500.0 chr1 2000 2500 geneB . - 2500.0 Using c2 if c6=='+' else c3 in the Compute tool. See if it works for you. - Russell >Date: Mon, 10 Oct 2011 17:36:58 +0200 >From: Hans-Rudolf Hotz <hrh(a)fmi.ch> >To: Ian Donaldson <Ian.Donaldson(a)manchester.ac.uk>, Daniel Blankenberg > <dan(a)bx.psu.edu>, "galaxy-user(a)lists.bx.psu.edu" > <galaxy-user(a)lists.bx.psu.edu> >Subject: Re: [galaxy-user] Q about 'Compute' tool >Message-ID: <4E93111A.4060302(a)fmi.ch> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > >On 10/10/2011 04:45 PM, Ian Donaldson wrote: >> Thanks, but not quite what i need. >> >> If i start with two intervals: >> chr1 500 1000 geneA . + >> chr1 2000 2500 geneB . - >> >> I want to add via, e.g. 'Compute', the TSS position to the end of each >>line. The desired result being: >> >> chr1 500 1000 geneA . + 500 >> chr1 2000 2500 geneB . - 2500 >> >> This is because geneA is on the '+' strand and geneB is on the '-' >>strand. >> > >Hi Ian > >Have you tried > >"Filter and Sort"-> "Filter" data on any column using simple expressions > >and create two lists containing all genes on the '+' strand and alles >genes on the '-' strand. > >followed by >"Text Manipulation"-> "Cut" columns from a table > > using 'c1,c2,c3,c4,c5,c6,c2' for the list with all genes on the '+' > strand > > and > > using 'c1,c2,c3,c4,c5,c6,c3' for the list with all genes on the '-' > strand > > >and then you can create a single list again with > >"Text Manipulation"-> "Concatenate" datasets tail-to-head > > >I guess this is waht you want, isn't-it? > > >Regards, Hans > > >> Thanks, >> Ian >> ________________________________ >> From: Daniel Blankenberg [dan(a)bx.psu.edu] >> Sent: 10 October 2011 14:34 >> To: Ian Donaldson >> Cc: galaxy-user(a)lists.bx.psu.edu >> Subject: Re: [galaxy-user] Q about 'Compute' tool >> >> Hi Ian, >> >> Under Operate on Genomic Intervals, you can try the "Get Flanks" tool; >>you can request upstream, downstream, or both of your provided regions. >>Please let us know if you need additional assistance. >> >> >> Thanks for using Galaxy, >> >> Dan >> >> >> On Oct 10, 2011, at 6:35 AM, Ian Donaldson wrote: >> >> Hi, >> >> Can 'if' statements by used in 'Text manipulation'> 'Compute'? >> >> The reason is that i have a interval file of UCSC genes, i want to >>identify the TSS of each and make a new interval reflecting the TSS >>position for each gene. But because the TSS of a '-' stranded gene is >>actually the 'end' coord i want to be able to check the strand in the >>compute statement. >> >> Is this possible or is there an easier way to do this inside GALAXY? >> >> Thank you, >> Ian >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.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/ >> >> >> >> >> >> ___________________________________________________________ >> 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 mailing list >galaxy-user(a)lists.bx.psu.edu >http://lists.bx.psu.edu/listinfo/galaxy-user > > >End of galaxy-user Digest, Vol 64, Issue 9 >******************************************

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version tophat and cufflinks
by dongdong zhaoweiming 11 Oct '11

11 Oct '11

Hi, May I ask what is the version of TopHat and cufflinks in the galaxy? Thanks a lot! weimin zhao

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select tophat and cufflinks
by dongdong zhaoweiming 10 Oct '11

10 Oct '11

Hi, I'm a user of galaxy.As I know, when TopHat and Cufflinks are supported through Galaxy, its version is 1.1.1 and 0.9.3,respectively. But now, the present version of TopHat and cufflinks is 1.3.2 and 1.1.0, which have some improvement over the previous version. I have a RNA-Seq reads about pig and I want to assemble my transcripts using the latest version of tophat and cufflinks. I don't know the present version of tophat and cufflinks in the galaxy or galaxy test, so what should I do if the version is the same as the previous one based on my poor bioinformatics background. Thanks a lot! weimin zhao

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Q about 'Compute' tool
by Ian Donaldson 10 Oct '11

10 Oct '11

Hi, Can 'if' statements by used in 'Text manipulation' > 'Compute'? The reason is that i have a interval file of UCSC genes, i want to identify the TSS of each and make a new interval reflecting the TSS position for each gene. But because the TSS of a '-' stranded gene is actually the 'end' coord i want to be able to check the strand in the compute statement. Is this possible or is there an easier way to do this inside GALAXY? Thank you, Ian

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Cost
by Lizex Husselmann 10 Oct '11

10 Oct '11

Hi Just a general question. How much is the cost of using the cloud on amazon, it says "pay-as-you-use". Can somebody give me a figure? Lizex Disclaimer This message is confidential and may be covered by legal professional privilege. It must not be read, copied, disclosed or used in any other manner by any person other than the addressee(s). Unauthorised use, disclosure or copying is strictly prohibited and may be unlawful. The views expressed in this email are those of the sender, unless otherwise stated. If you have received this email in error, please contact ARC Service Desk immediately. (mailto:Servicedesk@arc.agric.za) To report incidents of fraud and / or corruption in the ARC use our Ethics Hotline by: Phone number : 0800 21 20 56 Fax number : 0800 200 796 Email address : fraud(a)kpmg.co.za For more information on the ARC Ethics Hotline, please visit our website at www.arc.agric.za.

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Problem uploading files to Cloudman Galaxy
by Kevin Williamson 09 Oct '11

09 Oct '11

Hello, I seem to be unable to upload .fna files (eg, ~19 Mb in size) to a Cloudman Galaxy instance on an Amazon EC2 cluster [AMI = galaxy-cloudman-2011-03-22 (ami-da58aab3)]. I know that I can interact w/ the instance since I'm able to create/save workflows and add them to the tools menu. However, when I attempt to upload data files (stored on the computer I'm working at), the upload seems to hang in the perpetually uploading state. The .fna files CAN be quickly uploaded to the Penn State Galaxy, so I know there's no issue w. the files themselves. Has anyone else encountered this issue, and if so, what did you do to work around it? Any ideas/tips would be greatly appreciated. Thank you in advance, kevin

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Subscribing to Job Status Events
by Oren Livne 06 Oct '11

06 Oct '11

Dear All, Does Galaxy provide a way for a client app to subscribe to job status change notifications? Best would be a web service that lists the currently running jobs (for the current user / all users) and their status. Thank you so much, Oren

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QUESTION
by dtrejo＠ira.cinvestav.mx 06 Oct '11

06 Oct '11

I WANT TO ALIGNMENT MILLIONS OF SEQUENCES FROM A sRNA LIBRARY WITH A SMALL GENOME (2600 BASES). HOW CAN I DO THIS ALIGNMENT IN GALAXY?. I HAVE TRIED WITH MULTIPLE ALIGNMENTS FROM TOOLS, BUT I CAN NOT SELECT BOTH FILES. THANKS FOR YOUR HELP DIANA TREJO -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Possible to browse local filesystem
by alessandro albiero 06 Oct '11

06 Oct '11

Dear all, We are setting up a galaxy istance on our server (HPC Cluster with torque and PBS) for internal use. Our problem is that we manage only NGS data (SOLiD and Illumina Data) that are already stored on the server. When we connect to galaxy with our clients we are not able to browse the server file system. Having the possibility to browse the server filesystem would be the best solution for us!! We have look for this funtion but it seems it is not possible... Now, we tried to set up the user directory but adding new file and re-uploading the dir we found duplicated files (it seems that galaxy re-upload every time all the files ignoring if some are already present. This method is OK for us but how can we avoid the file duplications ? In a presentation found on web (blankenberg_pittsburg_2001), we saw that there is the possibility to automatically upload the sequenced reads on Galaxy (and let them available to all our user). Where can we find information for doing this ? All the best Alessandro -- ****************************** Alessandro Albiero Bioinformatics Lab CRIBI-Padua University Viale G. Colombo, 3 35121 Padova-Italy http://genomics.cribi.unipd.it http://genomics.cribi.unipd.it/index.php/User:Albiero Phone. +39. 049 827-6165 Fax. +39. 049 827-6159 ********************************

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