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Question: How can I plot alignment between fastq reads and reference sequence?
2
gravatar for MAPK
2.6 years ago by
MAPK • 1.6k
MAPK • 1.6k wrote:

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 • 2.2k views
ADD COMMENT • link •
modified 2.6 years ago by Sean Davis ♦ 26k • written 2.6 years ago by MAPK • 1.6k

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

ADD REPLY • link modified 2.6 years ago • written 2.6 years ago by genomax ♦ 90k
4
gravatar for Sean Davis
2.6 years ago by
Sean Davis ♦ 26k
National Institutes of Health, Bethesda, MD
Sean Davis ♦ 26k wrote:

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.
ADD COMMENT • link modified 2.6 years ago • written 2.6 years ago by Sean Davis ♦ 26k

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

ADD REPLY • link written 2.6 years ago by MAPK • 1.6k
1

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

ADD REPLY • link written 2.6 years ago by WouterDeCoster ♦ 44k

Got it. Thank you so much.

ADD REPLY • link written 2.6 years ago by MAPK • 1.6k
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