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
Kenneth
From the cuffmerge output, using merged.gtf instead of transcripts.gtf in the command for cuffdiff solved the problem.
Hi Kenneth,
I am running into this issue despite providing merged.gtf from Cuffmerge. Ever happened?
It helps if you print the command and the output as I did above. The only time it happened was in the situation above and was resolved with merged.gtf. Is your command the same as mine (above)?
Usage: cuffdiff [options] <transcripts.gtf> <sample1_hits.sam> <sample2_hits.sam> [... sampleN_hits.sam] Supply replicate SAMs as comma separated lists for each condition: sample1_rep1.sam,sample1_rep2.sam,...sample1_repM.sam
NB: each condition is separated by a space, but each replicate in each condition is separated by a comma (no space)
If different: Where is it different --> could that be the problem
If the same: Something wrong with input files
Found the answer. I posted it here It seems contrast file creates a problem when comparing only two samples.
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