Tweet
A recent paper suggests that cuffdiff 2 is not very sensitive and an overall poor choice for detecting differential expression in RNA-seq studies. Do you agree? Which option would you choose?
This paper looks at the issue empirically and suggests Limma: Comparison of software packages for detecting differential expression in RNA-seq studies (2013) Brief Bioinform doi: 10.1093/bib/bbt086 <http://bib.oxfordjournals.org/content/early/2013/12/02/bib.bbt086.long>
The paper analyzes GAII data... do you think the same would hold true for 50SE or 150PE Hiseq data?
The paper also analyzes human and mouse data. What about yeast or Arabidopsis?
This paper looks at the issue empirically and suggests Limma: Comparison of software packages for detecting differential expression in RNA-seq studies (2013) Brief Bioinform doi: 10.1093/bib/bbt086 <http://bib.oxfordjournals.org/content/early/2013/12/02/bib.bbt086.long>
The paper analyzes GAII data... do you think the same would hold true for 50SE or 150PE Hiseq data?
The paper also analyzes human and mouse data. What about yeast or Arabidopsis?