galaxy-user-requ...@lists.bx.psu.edu wrote:
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Not doing this greatly increases the number of emails that match search >queries, but that aren't actually informative. > >Today's Topics: > > 1. Convert SOLiD data (lishiyong) > 2. Re: biomart plugin (Greg Von Kuster) > 3. Re: Convert SOLiD data (Ryan Golhar) > 4. Re: Convert SOLiD data (Jennifer Jackson) > 5. Re: Sort & index SAM-files automatically (Ryan Golhar) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Mon, 28 Mar 2011 11:35:15 +0800 >From: "lishiyong" <lishiy...@genomics.org.cn> >To: "galaxy-user" <galaxy-user@lists.bx.psu.edu> >Subject: [galaxy-user] Convert SOLiD data >Message-ID: <201103281135102031...@genomics.org.cn> >Content-Type: text/plain; charset="us-ascii" > >Hello! > I convert SOLiD csfasta- and qual-files to fastq-files ,I want to use > the fastq-files to do denovo with SOAPdenovo.because the SOLiD de novo > accessory tools Require large memory .But ,I find that there're some question > for the converting . >for example: >T02023221102101032002002030011232121133222233311200 ��> >AGAGTGGCCAGCACATGAAGAAGATAACCGTGCGCCTTGGGGTTTCCGAA > >But I think it should to be TCCTAGACAAGTTGGCTTTCCCTTAAACAGCTGACATAGAGATATGTCCC > Who knows the reason about this. >2011-03-28 > > > >lishiyong >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: ><http://lists.bx.psu.edu/pipermail/galaxy-user/attachments/20110328/43b70c8a/attachment-0001.html> > >------------------------------ > >Message: 2 >Date: Mon, 28 Mar 2011 08:57:49 -0400 >From: Greg Von Kuster <g...@bx.psu.edu> >To: Andrea Edwards <edwar...@cs.man.ac.uk> >Cc: galaxy-user@lists.bx.psu.edu >Subject: Re: [galaxy-user] biomart plugin >Message-ID: <a3348bc1-7c00-4b8a-9313-de8444f44...@bx.psu.edu> >Content-Type: text/plain; charset="us-ascii" > >Hello Andrea, > >Make a copy of the ~/tools/data_source/biomart.xml for your local biomart >install, and change the action in the following tag to point to it. > ><inputs action="http://www.biomart.org/biomart/martview"; check_values="false" >method="get" target="_top"> > >Then add your new biomart tool wrapper to your tool_conf.xml file and start up >your Galaxy instance. > >For details about adding a new tool, see >https://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial. > >Greg Von Kuster > >On Mar 26, 2011, at 10:19 AM, Andrea Edwards wrote: > >> Hello >> >> I have looked at the biomart plugin for Galaxy and this seems to allow >> access to marts on the biomart central server. >> Is there anyway to use this plugin to access a biomart on my server if I >> can't make my biomart available on the biomart central server. >> >> If not, would it be possible to achieve this with galaxy tools. I've heard >> of galaxy tools but never made one so I don;t know what is involved. >> >> Failing that would i be able to use the biomart plugin to access my server >> if I had a local installation of galaxy >> >> >> thanks >> ___________________________________________________________ >> 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/ > >Greg Von Kuster >Galaxy Development Team >g...@bx.psu.edu > > > >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: ><http://lists.bx.psu.edu/pipermail/galaxy-user/attachments/20110328/3ebdda80/attachment-0001.html> > >------------------------------ > >Message: 3 >Date: Mon, 28 Mar 2011 09:53:56 -0400 >From: Ryan Golhar <golha...@umdnj.edu> >To: lishiyong <lishiy...@genomics.org.cn> >Cc: galaxy-user <galaxy-user@lists.bx.psu.edu> >Subject: Re: [galaxy-user] Convert SOLiD data >Message-ID: <4d9092f4.9040...@umdnj.edu> >Content-Type: text/plain; charset="windows-1252"; Format="flowed" > >Lishiyong, > >You should not convert colorspace to base space prior to aligning reads. > The reason for this is that if there is an error in one of the color >calls, it will effect all the downstream color calls. > >Instead, you should use an aligner that will do the assembly in >color-space instead. I know there are a few out there, but don't know >them off the top of my head. > >Ryan > >On 3/27/11 11:35 PM, lishiyong wrote: >> Hello! >> >> I convert SOLiD csfasta- and qual-files to fastq-files ,I want to use >> the fastq-files to do denovo with *SOAPdenovo*.because the SOLiD de novo >> accessory tools Require large memory .But ,I find that there're some >> question for the converting . >> >> for example: >> >> T02023221102101032002002030011232121133222233311200 ??> >> AGAGTGGCCAGCACATGAAGAAGATAACCGTGCGCCTTGGGGTTTCCGAA >> But I think it should to be >> TCCTAGACAAGTTGGCTTTCCCTTAAACAGCTGACATAGAGATATGTCCC Who knows the reason >> about this. >> 2011-03-28 >> ------------------------------------------------------------------------ >> lishiyong >> >> >> >> ___________________________________________________________ >> 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/ > >-- >CONFIDENTIALITY NOTICE: This email communication may contain private, >confidential, or legally privileged information intended for the sole >use of the designated and/or duly authorized recipient(s). If you are >not the intended recipient or have received this email in error, please >notify the sender immediately by email and permanently delete all copies >of this email including all attachments without reading them. If you are >the intended recipient, secure the contents in a manner that conforms to >all applicable state and/or federal requirements related to privacy and >confidentiality of such information. > >-------------- next part -------------- >A non-text attachment was scrubbed... >Name: golharam.vcf >Type: text/x-vcard >Size: 384 bytes >Desc: not available >URL: ><http://lists.bx.psu.edu/pipermail/galaxy-user/attachments/20110328/e73b87f8/attachment-0001.vcf> > >------------------------------ > >Message: 4 >Date: Mon, 28 Mar 2011 06:57:06 -0700 >From: Jennifer Jackson <j...@bx.psu.edu> >To: lishiyong <lishiy...@genomics.org.cn> >Cc: galaxy-user <galaxy-user@lists.bx.psu.edu> >Subject: Re: [galaxy-user] Convert SOLiD data >Message-ID: <4d9093b2.6090...@bx.psu.edu> >Content-Type: text/plain; charset=windows-1252; format=flowed > >Hello Lishiyong, > >Just to confirm, the conversion was performed at Galaxy main using "NGS: >QC and manipulation -> Convert SOLiD output to fastq"? With the option >"double encode = yes"? If so, the output appears to be correct. > >quote from tool help: > >"Double encode? - converts color calls (0123.) to pseudo-nucleotides >(ACGTN). Not necessary for bowtie. Required for BWA." > >Please let us know if we can help more, > >Best, > >Jen >Galaxy team > >On 3/27/11 8:35 PM, lishiyong wrote: >> Hello! >> >> I convert SOLiD csfasta- and qual-files to fastq-files ,I want to use >> the fastq-files to do denovo with *SOAPdenovo*.because the SOLiD de novo >> accessory tools Require large memory .But ,I find that there're some >> question for the converting . >> >> for example: >> >> T02023221102101032002002030011232121133222233311200 ??> >> AGAGTGGCCAGCACATGAAGAAGATAACCGTGCGCCTTGGGGTTTCCGAA >> But I think it should to be >> TCCTAGACAAGTTGGCTTTCCCTTAAACAGCTGACATAGAGATATGTCCC Who knows the reason >> about this. >> 2011-03-28 >> ------------------------------------------------------------------------ >> lishiyong >> >> >> >> ___________________________________________________________ >> 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 > > >------------------------------ > >Message: 5 >Date: Mon, 28 Mar 2011 09:56:51 -0400 >From: Ryan Golhar <golha...@umdnj.edu> >To: j.seggew...@ifg.uni-muenster.de >Cc: galaxy-user@lists.bx.psu.edu, Jochen Seggewi? > <jochen.seggew...@ifg.uni-muenster.de> >Subject: Re: [galaxy-user] Sort & index SAM-files automatically >Message-ID: <4d9093a3.5040...@umdnj.edu> >Content-Type: text/plain; charset="windows-1252"; Format="flowed" > >Jo, > >Use the SAM Tools SAM-TO-BAM tool in Galaxy to convert your SAM file to >a BAM file. > >Ryan > > >On 3/25/11 10:35 AM, Jochen Seggewi? wrote: >> Hi! >> >> Thank you for your reply. >> >> So that means, I should convert the csfasta & qual to fastq, map it with >> Bowtie, get an SAM, convert it to BAM and then index that BAM? >> How can I index BAM using GALAXY? >> I haven?t found a way to get a BAM directly from GALAXY using csfasta & >> qual as input files. >> >> Best regards >> >> Jo >> >> Am 3/25/2011 3:13 PM, schrieb Jim Robinson: >>> Hi Jo, >>> >>> To short-circuit confusion I'll jump in here. I'm the developer of >>> IGV and igvtools, the sorting and indexing for SAM files was added >>> long ago, even before indexed BAM files were possible from Java >>> programs. The recommendation now is to convert to BAM and index >>> that, although SAM files still work. If the galaxy community would >>> like the SAM option I'm happy to have igvtools wrapped as a module, >>> and will help with that. >>> >>> BTW, I also have some code (xml) to wrap IGV itself as a Galaxy >>> visualizer, contributed to me by a user. As I don't have a private >>> Galaxy installation I'm unable to test it myself, but can make it >>> available if anyone is interested. >>> >>> Jim >>> >>> >>>> Hello! >>>> >>>> I convert SOLiD csfasta- and qual-files to fastq-files and map those >>>> against Hg19 (Bowtie). >>>> I would like to use the resulting sam-files in the IGV browser (Broad >>>> Institute). >>>> Therefore, the sam-file need to be sorted an indexed. This could be >>>> done using the ?igvtools?. >>>> However, it would be nicer if this sorting and indexing could be done >>>> automatically using GALAXY. >>>> I guess that it is certainly possible ? but I do not know how. >>>> Could anybody let me know how it works and what function I have to >>>> use, respectively? >>>> How can I sort the sam-file the correct way? >>>> >>>> Thank you in advance. >>>> >>>> Best regards >>>> >>>> Jo >>>> ___________________________________________________________ >>>> 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/ >>> >>> >>> ___________________________________________________________ >>> 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/ >> >> >> ___________________________________________________________ >> 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/ > >-- >CONFIDENTIALITY NOTICE: This email communication may contain private, >confidential, or legally privileged information intended for the sole >use of the designated and/or duly authorized recipient(s). If you are >not the intended recipient or have received this email in error, please >notify the sender immediately by email and permanently delete all copies >of this email including all attachments without reading them. If you are >the intended recipient, secure the contents in a manner that conforms to >all applicable state and/or federal requirements related to privacy and >confidentiality of such information. > >-------------- next part -------------- >A non-text attachment was scrubbed... >Name: golharam.vcf >Type: text/x-vcard >Size: 384 bytes >Desc: not available >URL: ><http://lists.bx.psu.edu/pipermail/galaxy-user/attachments/20110328/a9c1d7be/attachment.vcf> > >------------------------------ > >_______________________________________________ >galaxy-user mailing list >galaxy-user@lists.bx.psu.edu >http://lists.bx.psu.edu/listinfo/galaxy-user > > >End of galaxy-user Digest, Vol 57, Issue 26 >******************************************* ___________________________________________________________ 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/
