I have a fastq file and a fasta file with one sequence. I want to plot a figure to show all the reads in fastq file aligned to the fasta file as shown in the figure below. I want to plot for both plus and minus strands. How can I do this (preferably using R)? Thank you for your help. 
Plot I want:
https://ibb.co/eV7EDx


Just a suggestion:

1. Align your fastq files against the fasta file, perhaps using bwa or bowtie2 outside of R.
2. Read the resulting BAM files into R using the GenomicAlignments Bioconductor package.
3. Visualize data using the Gviz Bioconductor package. 

