Question: Coverage for specific genes and exons
gravatar for bryantl
2.4 years ago by
United States
bryantl90 wrote:

I am using a whole exome sequencing dataset to look for potential pathogenic mutations. Overall, I have good coverage, but some regions of interest do not have good coverage and generate a false negative result. Is there a way to check coverage in a list of genes using galaxy to know if any have poor coverage? Right now I am checking by looking at the genes of interest in the UCSC genome browser, but that is very time consuming. Any suggestions are appreciated.

galaxy bam • 782 views
ADD COMMENTlink modified 2.4 years ago by Jennifer Hillman Jackson25k • written 2.4 years ago by bryantl90
gravatar for Jennifer Hillman Jackson
2.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The tool groups DeepTools and BEDTools at have several tool options for calculating coverage in BAM datasets. See the tool forms for links to usage help and more.

All of these tools are also available in the Tool Shed for use in a local or cloud Galaxy.

Others are welcome to comment about their favorite tools in these groups or alternates!

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.4 years ago by Jennifer Hillman Jackson25k
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