Percent/Fraction/Number of Bases vs. Read Depth plots - How to generate ?

[medalofhonour]

Hi,

I wish to generate a percentage of bases vs. read depth plot for my data. An example of such a plot (Figure 1B) is here in the following paper :

http://www.biomedcentral.com/1471-2164/13/341

Please let me know if there are any tools that can help me generate this plot quickly ? I hope there are some packages in Bioconductor that can help me get this plot.

[ParthavJailwala]

Hi,

Under Methods, they have this blurb, maybe that helps:

Genome coverage

We counted the number of bases in the genome that were not covered by any reads (Coverage = 0) and those with less than 5x read coverage (Coverage <5x). SAMtools was used to generate coverage plots and bash/awk scripts were used for coverage counting.

Thanks
Parthav

Hi,

I wish to generate a percentage of bases vs. read depth plot for my data. An example of such a plot (Figure 1B) is here in the following paper :

http://www.biomedcentral.com/1471-2164/13/341

Please let me know if there are any tools that can help me generate this plot quickly ? I hope there are some packages in Bioconductor that can help me get this plot.