I have 2 fastq files and I generated BAM file (indexed and sorted) of some reads. I aligned them to a reference genome (hg19).
I am working with different primers.
FORWARD 1. TTGCCAGTTAACGTCTTCCTTCTCTCTCTG 2. CCCTTGTCTCTGTGTTCTTGTCCCCCCCA 3. TGATCTGTCCCTCACAGCAGGGTCTTCTCT 4. CACACTGACGTGCCTCTCCCTCCCTCCA REVERSE 1. GAGAAAAGGTGGGCCTGAGGTTCAGAGCCA 2. CCCCACCAGACCATGAGAGGCCCTGCGGCC 3. TGACCTAAAGCCACCTCCTTA 4. CCGTATCTCCCTTCCCTGATTA
Therefore I have different amplicons. How can I plot the coverage of these different amplicons. And what could explain big difference between them?
Thank you very much for your help.