I see that most workflows includes tophat --> cufflinks --> cuffcompare --> cuffdiff.
If I want to perform differential expression analysis on RNASEQ samples based on a known annotation (e.g. Ensembl GTF), can I simply do tophat --> cuffdiff (with the known gtf)?
What would be the difference if I were to do tophat --> cufflinks --> cuffcompare and use that output gtf in cuffdiff?
If I want to perform differential expression analysis on RNASEQ samples based on a known annotation (e.g. Ensembl GTF), can I simply do tophat --> cuffdiff (with the known gtf)?
What would be the difference if I were to do tophat --> cufflinks --> cuffcompare and use that output gtf in cuffdiff?
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