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

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

alignment
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updated by Sean Davis Sean Davis • written by MAPK MAPK

1 answer

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.
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written by Sean Davis Sean Davis

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

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written by MAPK MAPK

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

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written by WouterDeCoster WouterDeCoster

Got it. Thank you so much.

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written by MAPK MAPK

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