Workflow for de novo transcriptome + GO + DE, what you recommend ?

Romualdo · 03-28-2016, 02:06 PM

Hi, I'm working with non reference models and I'm in search of a good workflow for de novo assembly, mapping, GO annotation, Differential Gene Expression and outputing in graphics. Its preferable something close to a all-in-one solution, I know all true all-in-one probably be commercial, I give a look in to geneious, someone used to it ? It gives nice results ?

I tried SOAPdenovo-trans, but I don't know what mapper I should use with it.
Tried trinotate too, it worked well for me, I generated the .sqlite, and used the sqlitebrowser to navigate it, but the trinotateweb that come with the trinotate seems poor about graphic output.

Suggestions will be very appreciated.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
New to Bioinformatics - What language would you recommend?	America CT	Bioinformatics	2	02-15-2016 02:36 PM
Can you recommend a good R statistics help forum?	LeonDK	Bioinformatics	2	03-04-2015 03:40 AM
Recommend your fragmentation method for PE 100bp on HiSeq	mullican	RNA Sequencing	4	03-12-2013 12:52 PM
recommend a short reads simulator?	schönblick	Bioinformatics	6	09-20-2012 10:39 AM
RNAseq transcriptome analysis: workflow problem	lollysticky	Bioinformatics	4	06-16-2011 08:26 PM

03-28-2016, 02:06 PM	#1
Romualdo Junior Member Location: Brazil Join Date: Nov 2014 Posts: 6	Workflow for de novo transcriptome + GO + DE, what you recommend ? Hi, I'm working with non reference models and I'm in search of a good workflow for de novo assembly, mapping, GO annotation, Differential Gene Expression and outputing in graphics. Its preferable something close to a all-in-one solution, I know all true all-in-one probably be commercial, I give a look in to geneious, someone used to it ? It gives nice results ? I tried SOAPdenovo-trans, but I don't know what mapper I should use with it. Tried trinotate too, it worked well for me, I generated the .sqlite, and used the sqlitebrowser to navigate it, but the trinotateweb that come with the trinotate seems poor about graphic output. Suggestions will be very appreciated.