Can Galaxy Analyze Solid Xsq Dataset Except Csfasta/Qual Data?

Question: Can Galaxy Analyze Solid Xsq Dataset Except Csfasta/Qual Data?

5.5 years ago by

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 COMMENT • link •

modified 4.7 years ago by Chandran, Uma • 20 • written 5.5 years ago by Wang, Daqing • 10

5.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 5.5 years ago by Jennifer Hillman Jackson ♦ 25k

4.7 years ago by

Chandran, Uma • 20

Chandran, Uma • 20 wrote:

Are there mappers for SoLiD 5500 on Galaxy? If so, do they take csfasta files as input? Thanks Uma Chandran

ADD COMMENT • link written 4.7 years ago by Chandran, Uma • 20

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 REPLY • link written 4.7 years ago by Ian Donaldson • 120

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 REPLY • link written 4.7 years ago by Chandran, Uma • 20

Please log in to add an answer.

Similar posts • Search »