No CDS in Cuffdiff output !

Question

[dina.hesham139]

Hey,

I did and RNAseq analysis for 2 conditions, paired end experiments. Alignment was done with HISAT2 against hg38 and I followed cufflinks and cuffdiff for assembly and quantification.

When I used cummeRbund to analyze cuffdiff output, it give me this:

CuffSet instance with:
  2 samples
  60483 genes
  348565 isoforms
  143516 TSS
  0 CDS
  60483 promoters
  143516 splicing
  0 relCDS

Why did I get zero CDS?

Thanks

[Benn]

That's big news! Thanks for the announcement.

[Ram]

The "News" category is most relevant when you announce something useful to the bioinformatics world, such as a new major release of a popular software tool, or a release by NIH asking teams to stop doing the pet bioinformatician thing. What you have here is a question.

[343129339]

hi! Did you slove this problem? I have same problem. Alignment was done with HISAT2 too.my cuffdiff file only have result with gene and isofrms : CuffSet instance with: 2 samples 14164 genes 14164 isoforms 0 TSS 0 CDS 0 promoters 0 splicing 0 relCDS

I check the gtf file and option --dta-cufflinks. There is no error report. if you already slove the problem ,please tell me . Thanks!

[Ram]

Please don't add an answer unless you've solved the question (and hence you have an actual answer). Add a comment if you wish to say "me too".

I've moving your answer to a comment now.

[Matteo Schiavinato]

Did you check the GTF file by doing a simple grep "CDS" file.gtf ? If you don't have lines representing CDS, then you obviously don't have CDS in the computation. If you do it, do you find CDS lines? How many? is it a number which is comparable with the number of exon lines (it should be < or = to that).