Re: can galaxy analyze SOLiD XSQ dataset except csfasta/qual data?

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Re: can galaxy analyze SOLiD XSQ dataset except csfasta/qual data?

Chandran, Uma

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

 

Thanks

Uma Chandran


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Re: can galaxy analyze SOLiD XSQ dataset except csfasta/qual data?

Ian Donaldson
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: [hidden email] [[hidden email]] on behalf of Chandran, Uma [[hidden email]]
Sent: 11 March 2014 13:14
To: [hidden email]
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:

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Re: can galaxy analyze SOLiD XSQ dataset except csfasta/qual data?

Chandran, Uma

Thank you!

Uma Chandran

 

From: Ian Donaldson [mailto:[hidden email]]
Sent: Wednesday, March 12, 2014 5:04 AM
To: Chandran, Uma; [hidden email]
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: [hidden email] [[hidden email]] on behalf of Chandran, Uma [[hidden email]]
Sent: 11 March 2014 13:14
To: [hidden email]
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/