[maker-devel] MWAS: User Feedback

[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, "grind001 at umn.edu" <grind001 at umn.edu> 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, "grind001 at umn.edu" <grind001 at umn.edu> 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: grind001 at umn.edu
>>>
>>
>>