Re: [galaxy-user] can galaxy analyze SOLiD XSQ dataset except csfasta/qual data?
Thank you! Uma Chandran From: Ian Donaldson [mailto:ian.donald...@manchester.ac.uk] Sent: Wednesday, March 12, 2014 5:04 AM To: Chandran, Uma; galaxy-user@lists.bx.psu.edu Subject: 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.edumailto: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.edumailto: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] 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] 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] can galaxy analyze SOLiD XSQ dataset except csfasta/qual data?
Hi Daquing, No, Galaxy does not work with the data in this format and no tools have been donated to the tool shed by the data format authors to do the conversion. You'll have to convert before loading into Galaxy, but from there it can be prepped using tools in the group FASTQ Manipulation. There are also some mapping tools that use converted SOLiD data as input specifically, these can be used on the Test server https://test.g2.bx.psu.edu/ or a local or cloud Galaxy. http://getgalaxy.org http://usegalaxy.org/cloud Best, Jen Galaxy team On 6/13/13 3:53 PM, Wang, Daqing wrote: Hello, I wonder if Galaxy take SOLiD XSQ format data as input for mapping. I know it takes csfasta/qual data. Does anyone try this kind of analysis with SOLiD XSQ format? Any feedback and advice is appreciate it. Thank you! Daqing Wang** ___ 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 Galaxy Support and Training 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/
[galaxy-user] can galaxy analyze SOLiD XSQ dataset except csfasta/qual data?
Hello, I wonder if Galaxy take SOLiD XSQ format data as input for mapping. I know it takes csfasta/qual data. Does anyone try this kind of analysis with SOLiD XSQ format? Any feedback and advice is appreciate it. Thank you! Daqing Wang ___ 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/
