How To Extract the total number of Spliced junctions from several biological replicates

Question

[hana]

Hi All

I have 6 RNA-Seq datasets (biological replicates). How can extract the total number of spliced junctions from all samples?

Is it correct way to merged the all the gtf files using cuffmerge and then run HISAT extract_splice_sites.py on the merged gtf file?

Or I should extract the spliced junctions from each individual BAM file separately?

Thanks in advance