I am mapping the raw reads to the contigs generated by de novo assembly of the same reads and want to represent the read coverage in the form of graph..
If you want to visualize the coverage on top of your genome, you can use Artemis. You load your genome and annotation in Artemis and a BAM file. There it will let you see not only globally but which regions are getting a higher or lower coverage.
Cheers
@Arjun Sahoo I have the exact same suggestion as Dong . Yes，IGV is a powerful tool to visualize the bam file to see the coverage profiling of you reads. You need input the refence genome fasta file,a bam file and an index file atthe same time.
Or use bedtools `bedtools genomecov -bg -ibam > out.bedgraph` to generate a per-base read count, which you can then feed into IGV or plot in R
http://bedtools.readthedocs.io/en/latest/
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