Question: How can I plot alignment between fastq reads and reference sequence?
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MAPK • 1.7k 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
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modified 3.1 years ago
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Sean Davis ♦ 26k
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written
3.1 years ago by
MAPK • 1.7k
qualimap
(http://qualimap.bioinfo.cipf.es/ ) can be an option once you have the BAM file.