unmapped reads by Tophat can be aligned by Bowtie2

Question

[zhangzhenyusz]

I used Tophat to map my pair-end reads to hg19. I sorted my unmapped.bam file, converted it to sam file and extracted pairs into two seperate fastq files. Finally, I use these two fastq files as input to Bowtie2. Surprisingly, there are 40 percent aligned by Bowti2. I know Tophat uses Bowtie2 to align reads. So why are there reads that can be recognized by Bowtie2 but not Tophat?

[h.mon]

Could you post all your commands here? What were the settings for each aligner?

[zhangzhenyusz]

For tophat I used: tophat -G <ref> -o <output> <genome> <read_1> <read_2> Then I got both accepted_hits.bam and unmapped.bam. I sorted the unmapped, converted to sam, extracted pair-end reads to two files to form my new read_1 and read_2. Used Bowtie 2 to align and found almost 40% been mapped.