Options and the output do not seem to match well.

[nowandnow]

I have a few questions about stringtie options. I used one samples and I want to test '-e' option

Below is Description of the -e option. Note that if option -e is not used the reference transcripts need to be fully covered by reads in order to be included in StringTie's output.

so i used command like below "{path}/stringtie {sample}_sorted.bam --rf -p 20 -l {prefix} -o {path}/{sample}.gtf -G {path}/{gtfname}.gtf -A {path}/{name}.tab -C {path}/{name}.gtf"

Of course, if the transcripts was fully covered by reads, there would be no cov value of zero. But there were zero values.

1. Is this a small number of 0 because there are covers but too few??

Second question is different between non -e and -e options. "{path}/stringtie {sample}_sorted.bam --rf -p 20 -l {prefix} -o {path}/{sample}.gtf -G {path}/{gtfname}.gtf -A {path}/{name}.tab -C {path}/{name}.gtf -e"

When stringtie detected the same location, But there were different values. (a little bit difference cov)

2. Why result is look like this?

I saw results on the same location from using option -e but no output from options without -e because the reference transcripts did not to be fully covered by reads?

Last questions is -e option output is bigger than non -e option output.

3. Why -e option output don't have all the outputs of non -e option output??