Question: How can I plot alignment between fastq reads and reference sequence?
2
gravatar for MAPK
2.2 years ago by
MAPK1.5k
United States
MAPK1.5k 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 • 1.7k views
ADD COMMENTlink modified 2.2 years ago by Sean Davis26k • written 2.2 years ago by MAPK1.5k

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

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by genomax80k
4
gravatar for Sean Davis
2.2 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k 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 COMMENTlink modified 2.2 years ago • written 2.2 years ago by Sean Davis26k

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

ADD REPLYlink written 2.2 years ago by MAPK1.5k
1

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

ADD REPLYlink written 2.2 years ago by WouterDeCoster43k

Got it. Thank you so much.

ADD REPLYlink written 2.2 years ago by MAPK1.5k
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