Greetings.
I'm interested in looking, in detail, at the mapped coverage for NGS short read data onto a reference, using whole genome data. I'd like a good way to examine and quantify the coverage along a chromosome and compare this coverage among samples to look for areas with usually high- and low-coverage, and to see if these high- and low-coverage areas are common among samples. I know how to get basic mapped read data using SAMtools, and I can look at the data visually using Atermis, but I don't know how to do anything more sophisticated.
Any help is much appreciated, cheers!
I'm interested in looking, in detail, at the mapped coverage for NGS short read data onto a reference, using whole genome data. I'd like a good way to examine and quantify the coverage along a chromosome and compare this coverage among samples to look for areas with usually high- and low-coverage, and to see if these high- and low-coverage areas are common among samples. I know how to get basic mapped read data using SAMtools, and I can look at the data visually using Atermis, but I don't know how to do anything more sophisticated.
Any help is much appreciated, cheers!
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