Question: unmapped reads by Tophat can be aligned by Bowtie2
gravatar for zhangzhenyusz
2.8 years ago by
zhangzhenyusz20 wrote:

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?

chip-seq tophat bowtie2 • 992 views
ADD COMMENTlink modified 2.8 years ago by Alex Reynolds30k • written 2.8 years ago by zhangzhenyusz20

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

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by h.mon29k

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.

ADD REPLYlink written 2.8 years ago by zhangzhenyusz20
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