Hi all,
I am using cufflinks package to look for differentially spliced exons. The pipeline I followed is tophat -> cufflinks -> cuffmerge/cuffcompare(tried with both) -> cuffdiff.
Result on command line is like this :-
Performed 23758 isoform-level transcription difference tests
Performed 20313 tss-level transcription difference tests
Performed 18306 gene-level transcription difference tests
Performed 17903 CDS-level transcription difference tests
Performed 0 splicing tests
Performed 0 promoter preference tests
Performing 0 relative CDS output tests
Writing isoform-level FPKM tracking
Writing TSS group-level FPKM tracking
Writing gene-level FPKM tracking
Writing CDS-level FPKM tracking
Writing isoform-level count tracking
Writing TSS group-level count tracking
Writing gene-level count tracking
Writing CDS-level count tracking
Writing isoform-level read group tracking
Writing TSS group-level read group tracking
Writing gene-level read group tracking
Writing CDS-level read group tracking
Writing read group info
Writing run info
Command I used to run cuffdiff is :-
./cuffdiff --no-update-check -o day0 -p 2 -N -b /home/Vaibhav/Alt_transcriptome_data/ws230/ws230.fa -u merged_asm/merged.gtf /home/Vaibhav/Alt_transcriptome_data/new/again_X_day0/accepted_hits.bam /home/Vaibhav/Alt_transcriptome_data/new/again_Y_day0/accepted_hits.bam
I have no replicates of the sample. Now I am getting some differential results for gene, cds and isoform but getting nothing for splicing and promoter something I am interested in. I also tried lowering c option till 2, but got the same result.Can someone please suggest me what should I do so that cuffdiff performs splicing tests.
Really in need of the differential spliced exons for my data.
Thanks a lot
I am using cufflinks package to look for differentially spliced exons. The pipeline I followed is tophat -> cufflinks -> cuffmerge/cuffcompare(tried with both) -> cuffdiff.
Result on command line is like this :-
Performed 23758 isoform-level transcription difference tests
Performed 20313 tss-level transcription difference tests
Performed 18306 gene-level transcription difference tests
Performed 17903 CDS-level transcription difference tests
Performed 0 splicing tests
Performed 0 promoter preference tests
Performing 0 relative CDS output tests
Writing isoform-level FPKM tracking
Writing TSS group-level FPKM tracking
Writing gene-level FPKM tracking
Writing CDS-level FPKM tracking
Writing isoform-level count tracking
Writing TSS group-level count tracking
Writing gene-level count tracking
Writing CDS-level count tracking
Writing isoform-level read group tracking
Writing TSS group-level read group tracking
Writing gene-level read group tracking
Writing CDS-level read group tracking
Writing read group info
Writing run info
Command I used to run cuffdiff is :-
./cuffdiff --no-update-check -o day0 -p 2 -N -b /home/Vaibhav/Alt_transcriptome_data/ws230/ws230.fa -u merged_asm/merged.gtf /home/Vaibhav/Alt_transcriptome_data/new/again_X_day0/accepted_hits.bam /home/Vaibhav/Alt_transcriptome_data/new/again_Y_day0/accepted_hits.bam
I have no replicates of the sample. Now I am getting some differential results for gene, cds and isoform but getting nothing for splicing and promoter something I am interested in. I also tried lowering c option till 2, but got the same result.Can someone please suggest me what should I do so that cuffdiff performs splicing tests.
Really in need of the differential spliced exons for my data.
Thanks a lot
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