Different Results Of Tophat2 And Bowtie2

[bbm]

Hello all,

I ran the same fastq file with tophat2 and bowtie2, and got very different mapping rates. I wonder if any of you will help me on this puzzle. It is single-end, 60-100 bp after trimming. Thanks a lot!!
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My code for tophat2 alignment:

tophat -G /gpfs_share/hlibyar/hlibyar/tophat/Am_genome.gff3 -o tophat_output_WO_48h --no-novel-juncs Am_genome /gpfs_share/hlibyar/hlibyar/trim/WO_48h_ACAGTG_L003_R1_001.trimmed60.fastq

The summary showed:
Reads:
Input : 19571887
Mapped : 1013220 ( 5.2% of input)
of these: 14267 ( 1.4%) have multiple alignments (14 have >20)
5.2% overall read mapping rate.

The code for bowtie2 alignment:
bowtie2 -x Am_genome -U /gpfs_share/hlibyar/hlibyar/trim/WO_48h_ACAGTG_L003_R1_001.trimmed60.fastq -S outputWO48trim60.sam

and the result is showing below:

19571887 reads; of these:

19571887 (100.00%) were unpaired; of these:

15594391 (79.68%) aligned 0 times

3948682 (20.18%) aligned exactly 1 time

28814 (0.15%) aligned >1 times

20.32% overall alignment rate

[bbm]

I also understand Tophat is splice-aware. My data is transcriptome (mRNA), I expect Tophat to map at a similar rate to Bowtie. One difference is tophat maps reads that span splice junctions, right?