Hi friends !
I'm trying to analyze the result of differentially expressed genes (DEGs) between the cufflinks (Cuffdiff ) and the Trinity (EdgeR). I know that in a de novo pipeline you can use some tools, such as edger or Cuffdiff, but how to compare the results? De novo analysis is really good ?
I have the results of both analyzes, but how to check if this correct? the first step would be finding the relationship of genes (this gene of Trinity is equals this gene of Cufflinks).
I can work with isomorfs, as trinity results, but it's dificult to imply a gene relationship.
I can use Blast, between the isomorfs results, but Blast is a local aligners, i would try some global aligners. How about Exonerate, one splice aligner?
Exonerate try to find the best position of each isoform in the genoma fasta file.
My idea is compare the GTFs results, and find some overlaps. I have a GTF file of Cufflinks result and i can make a GTF file over exonerate result. After this, compare some positions in the same Chromossome, for validate.
Other question: Blast is the best method to compare isoforms of two diferents results, like Cufflinks and Trinity?
Some help is always welcome.
Thanks all, Lucas.