Hi,
I have a bam file that was generated by running bowtie2 version 2.3.5 using paired end metagenomic sequences. The bam file was then sorted and indexed using samtools Version: 1.9 (using htslib 1.9). And so I am trying to triple check if the #mapped reads identified by running samtools idxstats is accurate. According to samtools idxstats I have 2 scaffolds where none of the reads recruited to it while the rest of the reference scaffolds had actual counts even if they were low. I wonder if there was a way to determine the number of mapped reads for multiple scaffolds from an indexed bam file without using samtools idxstats, in case it is a software glitch. Additionally, what would the significance of having 0 mapped reads to a reference mean? And is that a "normal" finding?
Thank you in advance for your help and guidance.
