I am not sure if this is a bug, but I cannot find any documentation related to this issue. I am interested in assemblies new versions of transcriptomes and quantifying the samples used to generate them.
I am assembling the new transcriptomes using 4 biological replicates, the annotated genome and the annotated reference transcriptome (ref.gtf) for the species of interest. What I have done is generating the merged.gtf using Cuffmerge, and then, to get the expression levels, I used Cuffcompare using as gtf the new transcriptome assembled (merged.gtf).
In the results (xxx.tracking) I got high percentages of transcripts (not only the reference ones, but also for the newly assembled) with 0 FPKM and confidence intervals between 0 (FPKM_conf_lo) and some number above 0 (FPKM_conf_hi). What is the meaning of this? That there is low confidence for the FPKM estimation? If it is the case, what is the reason?
I also obtained transcripts with 0 values in the 3 parameters, which I understand they were not detected (they come from the ref.gtf file). Am I wrong?
I am not sure if this is a bug, but I cannot find any documentation related to this issue. I am interested in assemblies new versions of transcriptomes and quantifying the samples used to generate them.
I am assembling the new transcriptomes using 4 biological replicates, the annotated genome and the annotated reference transcriptome (ref.gtf) for the species of interest. What I have done is generating the merged.gtf using Cuffmerge, and then, to get the expression levels, I used Cuffcompare using as gtf the new transcriptome assembled (merged.gtf).
In the results (xxx.tracking) I got high percentages of transcripts (not only the reference ones, but also for the newly assembled) with 0 FPKM and confidence intervals between 0 (FPKM_conf_lo) and some number above 0 (FPKM_conf_hi). What is the meaning of this? That there is low confidence for the FPKM estimation? If it is the case, what is the reason?
I also obtained transcripts with 0 values in the 3 parameters, which I understand they were not detected (they come from the ref.gtf file). Am I wrong?