How cufflinks works?

[rozitaa]

Hi,

I have different RNA-seq samples which I want to compare them with each other. I am using cufflinks to compare the transcription level of each gene.

I am getting different number of total genes per sample. I was expecting the output of cufflinks would be all genes in the ref annotation file and FPKM shows the relevant abundance of appearance of each transcript (some number for those which exist and zero for those that not). As far as I know, "cufflinks has values for all provided transcripts". If I am right, it means only those that are exist in my sequencing data. I am also, getting zero for some of the FPKM. So I cannot conclude the zeros with the mentioned phrase.

I cannot understand why these are happening and how I can interpret and compare the result. Generally, I want to have an overview of how cufflinks works. I have read cufflinks paper but it was hard for me to hunt answers of these question out of it.

Any comments about it would be so helpful.

Thanks

[seqlearning]

Hi,

I have different RNA-seq samples which I want to compare them with each other. I am using cufflinks to compare the transcription level of each gene.

I am getting different number of total genes per sample. I was expecting the output of cufflinks would be all genes in the ref annotation file and FPKM shows the relevant abundance of appearance of each transcript (some number for those which exist and zero for those that not). As far as I know, "cufflinks has values for all provided transcripts". If I am right, it means only those that are exist in my sequencing data. I am also, getting zero for some of the FPKM. So I cannot conclude the zeros with the mentioned phrase.

I cannot understand why these are happening and how I can interpret and compare the result. Generally, I want to have an overview of how cufflinks works. I have read cufflinks paper but it was hard for me to hunt answers of these question out of it.

Any comments about it would be so helpful.

Thanks

Same here.
I asked my data mapping to a GTF with ~70 genes. Then I used cufflinks to deal with the mapped results, found only about 10 genes with non-zero FPKM.

[liweixie]

did you have reference gtf file for cufflinks.

[rozitaa]

Thanks, I found new gtf and fasta reference file and I think the whole problem caused because of the reference files!