What should I do with STAR two-pass novel splice junctions?

Question

[CTLong]

Hi,

I have a few relatively naive questions which I don't fully understand. I know that the STAR two-pass mode can detect for novel splice junctions on top of the annotations from GTF/GFF3 files. Let's say I run a STAR two-pass mapping, this generates three questions

1) Other than the ReadsPerGene.out.tab file, what other files or information is valuable from the STAR output, is there a file which records the novel splice junctions? 2) With the novel splice junction information, what can I do with this (ie. does this lead to the identification of a novel splice variants and transcript of a gene)? 3) Will there be differences in the Genecounts results with one-pass and two-pass mode, if quantification is performed on gene-level?

Thank you.