X is the position in genome, and Y is the read depth . while tools can do this work ?
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siyu •
It really depends on how comfortable you are in using plotting tools. You can use R or gnuplot and can make pretty cool figures. You can bin the genomic locations so that you can cover the whole chromosome in one plot. I generally use circos (http://circos.ca/tutorials/course/) and plotting tools from R. If you want to do it in an easy way you can use:
PS: You should wait for other people's reply too. They may suggest something really cool. I am not into plotting things.
I also like to use Hagfish https://github.com/mfiers/hagfish/wiki/Plots (because that one also shows regions where the insert size is too large or too small, suggesting a wrong assembly in that region)
You can try Gviz R/bioconductor https://www.bioconductor.org/packages/devel/bioc/vignettes/Gviz/inst/doc/Gviz.html
It cab be used to to plot Sequencing Depth directly from bam file.
Best wishes,
-Ahmed Alhendi
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This has been asked and answered many times already What tools/libraries do you use to visualize genomic feature data? How to plot read coverage over many different genomic regions? Genome wide plots in [R] Drawing chromosome ideogams with data just to name a few. Opting to close this question as it adds nothing new to the topic.