calculation of gene coverage

Question

[ameya4microbiology]

I am beginner in bioinformatics and working on NGS for my Ph.D. project. I have illumina and ONT reads of yeast. I would like to know the tool to combine or hybridize and after calculation how to calculate coverage of a specific gene of interest inserted in genomic DNA?

Answer 1

[prasundutta87]

Check out Qualimap bamqc (http://qualimap.conesalab.org/doc_html/analysis.html#bamqc)

Give your gene coordinates of interest as a GFF or BED file in the Regions file option (-gff, OR --feature-file). Hope this helps.