Hello dear one,
for my new project I would need sequence alignment tool to analyse RNA-seq data. I found that bowtie2 is a tool used in most of the previous studies and also bwa-mem is a tool does the same!
So, I was supposed to compare the both tools!
when I align (2GB +2GB fastq files) paired en reads, bowtie2 took 5131.879537 seconds . In other hand, bwa-mem took only 1041.879358 seconds. (bwa mem is so faster) I compared both of the output sam files, Its position, CIGAR, MRNM, MPOS are same only! flags are +/- 2 variations!
Anyone help me choose, which one? and what is the difference between them?
Thanks in advance!