I am performing a genome-guided transcriptome assembly with Stringtie.
Before the transcriptome assembly, I have mapped my paired-end reads of the same sample with HISAT2 and TopHat2 and for each mapping I performed the transcriptome assembly.
In my transcriptome assembly I noticed that in a region, Stingtie assembled only one transcript with HISAT mapped reads, while Stringtie assembled two transcripts with TopHat mapped reads. When I check this region, I noticed that HISAT mapped both mates of fragments and some mate are spliced-aligned supporting the reconstructed isofom. In the same region TopHat mapped only one mate of the fragment and the other mate is unmapped, so I did not have the spliced mate and I obtained two different isoforms instead of only one isoforms as HISAT.
Subsequently I performed the same analysis with a subset of reads of the same sample. I noticed that TopHat aligned in the same region both mate of the same fragment obtaining one isoform like the first mapping with HISAT.
I was wondering why TopHat did not map one mate of the fragment when HISAT is able to map both mates. In addition, how it can be explained that when I performed the analysis on a subset of reads TopHat is able to map both mates as HISAT.