Hi

I am currently working on RNA-seq using cufflinks, I am confused about the result of cufflinks when I used -G and -g option and run cufflinks without gtf

I found different number of genes and transcripts from my output results:

for the -G mode, I found 17,876 gens and 32,568 transcripts.

for the -g mode,I found 25,554 gens and 33,453 transcripts

without using gtf references file, I found 18,342 gees and 34,871 transcripts

Also I observed several new transcripts not listed in the result when I used -G mode where only used the known transcript. I also saw that some of known transcript from -G mode is not in the result using -g mode.

Which result is correct for reporting the number of genes and transcripts?

Many thanks for your suggestions