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6.7 years ago
zhangzhenyusz
▴
30
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?
Could you post all your commands here? What were the settings for each aligner?
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.