Don't understand three modes of TCGA STAR 2-pass

Question

[tomas4482]

I do not fully understand the difference between STAR 2-pass genome and STAR 2-pass transcriptome in GDC data portal.

They explained that the reference is different. Reads are aligned to genome sequence and transcriptome sequence respectively. But I still don't understand what the difference is. Usually when we perform alignment, we used e.g. Ensembl or Gencode annotations gtf or gff3 for primary contigs or choromosomes.

1. What is the exact annotation reference these modes used?

2. If I wish to detect splicing junctions (annotated and de novo), which mode should I choose?

Can anyone explain it a little bit for me? Thank you very much.

Answer 1

[Zhenyu Zhang]

1. gencode 36 now
2. there are splice junction files
3. genomic alignment is not dependent on gene model