I got an alignment-to-human obtained via BWA and I deduplicated the bam file. I would like to visualize the quality of the alignment with R in order to have complete control on the graphic.
samtools stats to get the basic information but how is the output formatted? I can see that
# Columns correspond to qualities and rows to cycles. First column is the cycle number.
but what are cycles? and do the columns represents the chromosomes of the reference genome? If yes, can I get the name of the chromosomes?