Question: Can Galaxy Analyze Solid Xsq Dataset Except Csfasta/Qual Data?
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gravatar for Wang, Daqing
5.5 years ago by
Wang, Daqing10
Wang, Daqing10 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
galaxy • 1.2k views
ADD COMMENTlink modified 4.7 years ago by Chandran, Uma20 • written 5.5 years ago by Wang, Daqing10
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gravatar for Jennifer Hillman Jackson
5.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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 -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
ADD COMMENTlink written 5.5 years ago by Jennifer Hillman Jackson25k
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gravatar for Chandran, Uma
4.7 years ago by
Chandran, Uma20 wrote:
Are there mappers for SoLiD 5500 on Galaxy? If so, do they take csfasta files as input? Thanks Uma Chandran
ADD COMMENTlink written 4.7 years ago by Chandran, Uma20
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 ________________________________ 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
ADD REPLYlink written 4.7 years ago by Ian Donaldson120
Thank you! Uma Chandran 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 ________________________________ To: galaxy-user@lists.bx.psu.edu<mailto: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
ADD REPLYlink written 4.7 years ago by Chandran, Uma20
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