Novel lncRNA identification and quantification RNA seq?

Question

[mathavanbioinfo]

Hello All, I am working on human novel lncRNA expression & quantification in different cell types, I build index files ( hg38) with & without --exon --splice-sites by Hisat2, Is there any differences are in the results of CPC2 tool.

Index files build with exon & splice sites

$ extract_splice_sites.py chrX_data/genes/chrX.gtf >chrX.ss $ extract_exons.py chrX_data/genes/chrX.gtf >chrX.exon $ hisat2-build --ss chrX.ss --exon chrX.exon chrX_data/genome/chrX.fa chrX_tran

Index files build without exon & splice sites $ hisat2-build chrX_data/genome/chrX.fa chrX_tran