I have single ended RNA-seq library data whose library is distributed among different lanes. After quality check and trimming, I have used this pipeline to estimate Alternative splicing events. Is this pipeline seems good to scientific community?

Mapping with Hisat2

hisat2 -p 8 --dta -x Indexed_genome -U Sample_A_1.fastq,Sample_A_2.fastq,Sample_A_3.fastq -S output_A.sam

Sam to bam

samtools sort -@ 8 -o output_A.bam output_A.sam

Assembly via StringTie

stringtie -p 8 -G genome_annotation.gtf -o output_A.gtf –l output_A output_A.bam

Alternative splicing via ASTALAVISTA

submitted output_A.gtf to ASTALAVISTA (http://genome.crg.es/astalavista/) and got results.

your feedback will be highly appreciated.