Question: Cuffdiff not performing tss, cds, splicing, promoter or CDS tests
0
gravatar for YaGalbi
3.3 years ago by
YaGalbi1.4k
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.4k wrote:

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

rna-seq cuffdiff • 1.4k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by YaGalbi1.4k
0
gravatar for YaGalbi
3.3 years ago by
YaGalbi1.4k
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.4k wrote:

From the cuffmerge output, using merged.gtf instead of transcripts.gtf in the command for cuffdiff solved the problem.

ADD COMMENTlink written 3.3 years ago by YaGalbi1.4k

Hi Kenneth,

I am running into this issue despite providing merged.gtf from Cuffmerge. Ever happened?

ADD REPLYlink written 3.1 years ago by Satyajeet Khare1.5k
1

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

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by YaGalbi1.4k

Found the answer. I posted it here It seems contrast file creates a problem when comparing only two samples.

ADD REPLYlink written 3.1 years ago by Satyajeet Khare1.5k
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