I have just run cuffdiff with the following command:
cuffdiff -p 4 -o cuffdiff_out -b [path]/genome.fa -u -L control,treated [path]/merged_transcripts.gtf C1.bam,C2.bam,C3.bam,C4.bam T1.bam,T2.bam,T3.bam
The final few lines of the terminal:
Processed 18749 loci. [*******] 100%
Performed 6777 isoform-level transcription difference tests
Performed 0 tss-level transcription difference tests
Performed 6250 gene-level transcription difference tests
Performed 0 CDS-level transcription difference tests
Performed 0 splicing tests
Performed 0 promoter preference tests
Performing 0 relative CDS output tests
How do I resolve this? I am required to analyse for differential alternative splicing.
EDIT: In the protocol paper the command actually uses the merged.gtf instead of the transcripts.gtf from the cuffmerge output) so Im giong to try that to see if there is a difference.
Thanks in advance