Re: MWAS: User Feedback

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

Re: MWAS: User Feedback

Carson Hinton Holt
MAKER won't really annotate those.  Transcriptome annotation is a very
different problem from genome annotation.  I'm CC'ing this to the MAKER
mailing list to see if anyone has good suggestion for transcriptome
annotation.

I would recommend using Repeatmasker to remove transposons from your
transcriptome set, and then InterProScan for domain identification and
maybe blast2go for GO term association.

--Carson
 



On 12-09-10 1:10 PM, "[hidden email]" <[hidden email]> wrote:

>I have assembled RNAseq transcripts. There's no genome assembly for our
>species right now, so I was trying to do an organized assembly pipeline
>and
>use your system.
>
>On Sep 10 2012, Carson Holt wrote:
>
>>Tell me a little more about your project.  Based on your brief
>>description
>>I think you might need a different tool.  MAKER doesn't assemble or
>>annotate transcriptomes (i.e. RNA only).  It works with de novo genome
>>assemblies to identify the genes from them (I.e entire chromosomes or
>>large fragments of chromosomes).  It can use RNA-seq result to help
>>annotate the genome but still requires a genome assembly.
>>
>>The online server will annotate maximum of 5 Mb at a time and it's slow
>>(mostly built for small jobs).  You will get 10-20 faster performance
>>locally.
>>
>>Thanks,
>>Carson
>>
>>
>>
>>On 12-09-10 12:17 PM, "[hidden email]" <[hidden email]> wrote:
>>
>>>Maker Web Annotation Service - User Feedback:
>>>---------------------------------------------
>>>Hi,
>>>
>>>I'm working on getting your software installed on my systems,  and have
>>>done a test run on your web page with a portion of my data.
>>>I have 150,000 contigs from a de novo assembly of our transcriptome.  Do
>>>you have room on your server for a large run?  or is this just a sample
>>>space to test the software?  I'm under some time constraints and an just
>>>checking and hoping to push this forward a bit faster.
>>>
>>>
>>>
>>>Best,
>>>Suzanne
>>>University of MN
>>>
>>>
>>>---------------------------------------------
>>>User: 1440
>>>First: Suzanne
>>>Last: Grindle
>>>Institution: University of Minnesota
>>>E-mail: [hidden email]
>>>
>>
>>


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|

Re: MWAS: User Feedback

Felix Bemm
hi suzanne,

the trinity assembler mailing list has some good ideas for that. You
could think about using an "intelligent" orf finder like transdecoder
(transdecoder.sourceforge.net). the predicted orfs can than be used for
an interpro and blast2go run. merge the interpro and the b2g run with
the built-in tool of blast2go. simply put the interpro xml's for each
orf of a given transcript into one file for that and use the built-in
import function of blast2go. this might help you to improve the GO
annotation. it also works with the b2g pipeline tool (which is much
faster). In addition, you could try to use interproscan standalone 5
(http://code.google.com/p/interproscan/) since it has an improved
support for nucleic acid sequences.

cheers
felix

Am 10.09.2012 19:21, schrieb Carson Holt:

> MAKER won't really annotate those.  Transcriptome annotation is a very
> different problem from genome annotation.  I'm CC'ing this to the MAKER
> mailing list to see if anyone has good suggestion for transcriptome
> annotation.
>
> I would recommend using Repeatmasker to remove transposons from your
> transcriptome set, and then InterProScan for domain identification and
> maybe blast2go for GO term association.
>
> --Carson
>
>
>
>
> On 12-09-10 1:10 PM, "[hidden email]" <[hidden email]> wrote:
>
>> I have assembled RNAseq transcripts. There's no genome assembly for our
>> species right now, so I was trying to do an organized assembly pipeline
>> and
>> use your system.
>>
>> On Sep 10 2012, Carson Holt wrote:
>>
>>> Tell me a little more about your project.  Based on your brief
>>> description
>>> I think you might need a different tool.  MAKER doesn't assemble or
>>> annotate transcriptomes (i.e. RNA only).  It works with de novo genome
>>> assemblies to identify the genes from them (I.e entire chromosomes or
>>> large fragments of chromosomes).  It can use RNA-seq result to help
>>> annotate the genome but still requires a genome assembly.
>>>
>>> The online server will annotate maximum of 5 Mb at a time and it's slow
>>> (mostly built for small jobs).  You will get 10-20 faster performance
>>> locally.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 12-09-10 12:17 PM, "[hidden email]" <[hidden email]> wrote:
>>>
>>>> Maker Web Annotation Service - User Feedback:
>>>> ---------------------------------------------
>>>> Hi,
>>>>
>>>> I'm working on getting your software installed on my systems,  and have
>>>> done a test run on your web page with a portion of my data.
>>>> I have 150,000 contigs from a de novo assembly of our transcriptome.  Do
>>>> you have room on your server for a large run?  or is this just a sample
>>>> space to test the software?  I'm under some time constraints and an just
>>>> checking and hoping to push this forward a bit faster.
>>>>
>>>>
>>>>
>>>> Best,
>>>> Suzanne
>>>> University of MN
>>>>
>>>>
>>>> ---------------------------------------------
>>>> User: 1440
>>>> First: Suzanne
>>>> Last: Grindle
>>>> Institution: University of Minnesota
>>>> E-mail: [hidden email]
>>>>
>>>
>>>
>
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>


--
Felix Bemm
Department of Bioinformatics
University of W├╝rzburg, Germany
Tel: +49 931 - 31 83696
Fax: +49 931 - 31 84552
[hidden email]

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org