This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Automating the creation of IGV style histogram coverage maps

Hello, I'm working on a pipeline using Bash, Python, and R to process metagenomic datasets. One of the features I want to incorporate is producing coverage maps for some hits depending on the read counts associated with them.

I know how to do this using IGV or UCSC genome browser and the necessary .bam and .bai files. However I want to automate this process so I won't need to manually do it each time. Some preliminary googling hasn't yielded much useful data. I was curious if anyone was aware of any Bash, Python, or R packages that have this same functionality?

Any help would be awesome, thanks!

genome alignment r python bash
• 1,479 views • link
updated by dariober dariober • written by cxr5298 • cxr5298

2 answers

I quickly wrote something like this using nextflow+ (samtools depth+R) a few weeks ago:

I imagine I should add another param to 'smooth' the curves.

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

If you are ok with R, have a look at Gviz. For something scriptable but with not very polished output see ASCIIGenome (disclaimer- I'm the author)

• 0 views • link
written by dariober dariober

Log in to answer this question.

More posts like this