I'm working on a project where I'm aligning fastq files that contain sequence information about a series of small ORfs (usually ~2 kb in size). These were all contained in bacterial entry vectors (i.e., plasmids).
I'm using bowtie2 to align these sequences, but would like to determine the pileups somehow.
Currently, I've tried using mpileup with samtools. However, since samtools works with diploid genomes, my questions are:
1) Would using samtools mpileup to determine pileup information be incorrect for a haploid organism? (Note that I'm not doing variant calling; I use SNVer to do variant calls).
2) If so, is there another program I can use to get pileup info for haploid organisms? Alternatively, is there anything I can do in samtools to specify ploidy? It doesn't seem to be an option right now.