How can I plot alignment between fastq reads and reference sequence?

Question

[MAPK]

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

[GenoMax]

qualimap (http://qualimap.bioinfo.cipf.es/ ) can be an option once you have the BAM file.

Answer 1

[Sean Davis]

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.

[MAPK]

Thank you Sean for your answer. So for the first step, should I just extract the aligned bam file from bowtie alignment?

[WouterDeCoster]

You just need to align the reads and use that bam file.

[MAPK]

Got it. Thank you so much.