What is the differences in index building by hisat with or without exon, splicing variant files?

Question

[mathavanbioinfo]

Hello All, I am working NGS data analysis, for building an index hisat list two option with or without exon, splicing variant file, what is the main differences are there. Which index file is suitable for novel lncRNA prediction

code $ extract_splice_sites.py chrX_data/genes/chrX.gtf >chrX.ss $ extract_exons.py chrX_data/genes/chrX.gtf >chrX.exon Second, build a HISAT2 index: $ hisat2-build --ss chrX.ss --exon chrX.exon chrX_data/genome/chrX.fa chrX_tran

Paper : Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown