How Can I Plot A Region'S Depth As Follow? While Tools Should I Use?

Question

[siyu]

X is the position in genome, and Y is the read depth . while tools can do this work ?

[Michael]

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.

Answer 1

[Ashutosh Pandey]

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:

1. IGV (http://www.broadinstitute.org/igv/).
2. Seqmonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
3. Grid Package in R (http://biobeat.wordpress.com/2012/12/18/plot-genome-coverage-graphs-using-grid-package-in-r/)

PS: You should wait for other people's reply too. They may suggest something really cool. I am not into plotting things.

[Philipp Bayer]

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)

Answer 2

[Ahmed Alhendi]

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