I have the sam files created and I wanted to check what's going on in these files. Here are some basic commands for checking if the alignments have run properly.
# used the grep command to search for lines of sequence containing a match to the given pattern (03 & reference genome)
grep -c ^ABC ABC12-03.sam
grep ^ABC ABC12-03.sam | cut -f 2 | sort | uniq -c
# viewed the bottom reads of SAM file for questions pertaining to individual/reference allignment (03)
tail ABC12-03.sam
samtools view -b -S -o ABC12-03.bam ABC12-03.sam
# used the grep command to search for lines of sequence containing a match to the given pattern (01 & reference genome)
grep -c ^ABC ABC12-01.sam
grep ^ABC ABC12-01.sam | cut -f 2 | sort | uniq -c