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.