Gain sequences after mapping reads to a reference genome

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Gain sequences after mapping reads to a reference genome

zwp112358
Hi all,
 
I would like to know if mapping reads to a reference genome, through galaxy, can generate the query genome sequence?
 
I had mapped my reads from Illumina sequencer to a reference genome through both BWA and Bowtie on Galaxy public server platform(https://main.g2.bx.psu.edu/root ).  As a result, i gained the SAM files. But, i can't find how to generate the resulted assemblied genome sequence.
 
Is there anyone know this? Any reply will be very appreciated.
 
Best regards.
 
Weiping
 

 
Weiping Zhang, Doctor candidate;
School of bioengineering, Jiangnan University;
Lihu Roads 1800#, WUXI, Jiangsu;
Zip Code: 214122

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Re: Gain sequences after mapping reads to a reference genome

Jen Hillman-Jackson
Hello Weiping,

The resulting SAM hits can be converted to intervals, and the intervals merged, and those regions extracted from the reference genome you mapped to.  The tools to use would be:
* NGS: SAM Tools -> Convert SAM to interval
* Operate on Genomic Intervals -> Merge (although you can explore other tools in this group)
* Fetch Sequences -> Extract Genomic DNA

Note that this would not include any variation included in the original mapped fastq data itself. If you are interested variation (SNPs or Indels or both) in your data, then you want to use a mapping tool like BWA (or Bowtie2 in a local or cloud Galaxy), followed by a variant analysis tools. Several tool groups in the "NGS:*" section are for this purpose, such as those in the group " NGS: SAM Tools" (Mpileup, etc.).

Hopefully this helps,

Jen
Galaxy team

On 4/27/13 10:19 PM, zwp112358 wrote:
Hi all,
 
I would like to know if mapping reads to a reference genome, through galaxy, can generate the query genome sequence?
 
I had mapped my reads from Illumina sequencer to a reference genome through both BWA and Bowtie on Galaxy public server platform(https://main.g2.bx.psu.edu/root ).  As a result, i gained the SAM files. But, i can't find how to generate the resulted assemblied genome sequence.
 
Is there anyone know this? Any reply will be very appreciated.
 
Best regards.
 
Weiping
 

 
Weiping Zhang, Doctor candidate;
School of bioengineering, Jiangnan University;
Lihu Roads 1800#, WUXI, Jiangsu;
Zip Code: 214122


___________________________________________________________
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/
Jennifer Hillman-Jackson
http://galaxyproject.org