I was running bowtie2 version 2.5.1 on a dataset of pair end reads, to a reference sequence.
I aligned the reads with bowtie2 and extract all the aligned reads with samtools view flage -F 4 -F 8 on the resulting sam file.
I aligned all these aligned reads in pair end mode with bowtie2 again to the same reference sequence, and bowtie2 showed not 100% reads are aligned: I found some of the reads aligned the first time did not align the second time.
Is there a way of explaining why this could happened? I did not put flags like -X or -I. The following are the command flags I used.
bowtie2 -x -1 -2 -S -p
Hi,
I was running bowtie2 version 2.5.1 on a dataset of pair end reads, to a reference sequence. I aligned the reads with bowtie2 and extract all the aligned reads with samtools view flage -F 4 -F 8 on the resulting sam file. I aligned all these aligned reads in pair end mode with bowtie2 again to the same reference sequence, and bowtie2 showed not 100% reads are aligned: I found some of the reads aligned the first time did not align the second time.
Is there a way of explaining why this could happened? I did not put flags like -X or -I. The following are the command flags I used. bowtie2 -x -1 -2 -S -p
Thank you!