As the title says, would appreciate if someone can give me a tip of tools you use when analyzing gene expressions.
Thanks in advance.
asked 15 Aug '12, 10:14
It depends on if you have a reference genome or not. If you have one, then you could use TopHat (http://tophat.cbcb.umd.edu/) as aligner, since it can detect splice junctions. Then you can use Cufflinks (http://cufflinks.cbcb.umd.edu/) to assemble transcripts and detect differential expression.
If you do not have a reference genome, you could use Trinity (http://trinityrnaseq.sourceforge.net/) to do a de novo assembly of the transcripts.
All the programs are available on Uppmax if you are running on that system. As always, there are as many opinions about which programs to use as there are users :)
answered 16 Aug '12, 10:59
I think that BWA could also be a very useful tool for mapping against a reference genome.It can handle gaps in the mapping which is not possible in Bowtie (Tophat is using Bowtie). Bowtie and BWA seems to be the fastest mappers around which is of course an issue when it comes to large scale NGS projects. If you decide to go for Bowtie you can follow this protocol published in Nature this year:
These protocols describe how to map with Bowtie and all the way up to identifying differentially regulated genes.
Trinity is wonderful for when you do not have a reference genome.
answered 12 Sep '12, 11:33
Thanks all for your answers!
answered 12 Sep '12, 13:10