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?
Question: unmapped reads by Tophat can be aligned by Bowtie2
2.8 years ago by
zhangzhenyusz • 20
zhangzhenyusz • 20 wrote:
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