Hello everyone!
I am using a pipeline to analyze RNAseq data from solid 5500.
Firstly I aligned my reads with TopHat obtaining .bam files.
Now I am running Cufflinks 1.3.0.
I was wondering why I could not get any FPKM values different from zero when I use the annotation .gtf file.
I tried to run Cufflinks without any .gtf file and in this case I succeded in obtaining FPKM values.
Do you have any idea?
Thanks
I am using a pipeline to analyze RNAseq data from solid 5500.
Firstly I aligned my reads with TopHat obtaining .bam files.
Now I am running Cufflinks 1.3.0.
I was wondering why I could not get any FPKM values different from zero when I use the annotation .gtf file.
I tried to run Cufflinks without any .gtf file and in this case I succeded in obtaining FPKM values.
Do you have any idea?
Thanks
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