why don‘t bowtie2 produce sam files directly？

[sunhaifeng123]

Hi：
In your process : after split the raw fastqs into dna.fasta and rna.fastq, while mapping them with genome.fasta , you use bowtie2 and right after samtools convert to bam.
my question is : why don't u produce sam files and 'samtools view -F 4 ' and awk to make theme simple.txt files?
I think if doing this we can save time and memory, looking forword to your reply!
any help will be grateful!
Haifeng Sun
China NanJing Medical University
20181114