Question: using GenomeCoverageBed tool
gravatar for A
5.0 years ago by
A3.7k wrote:


i am in windows then i used galaxy to convert my bam file to bed, when i was creating a graph of genome coverage by my resulted bed file, i noticed i should install bedtools on my system...:(

is any other way to use GenomeCoverageBed tool in windows or to convert the resulted bed file in a format to be visualized???

i think bedtools just works on unix, linux and os not windows...

rna-seq • 2.1k views
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by A3.7k

Hi Dan,

i went to galaxy but it said that i need to install bedtools in my system first to use genomecov bedgraph and histogram...but i cant installed bedtools on windows

i went to RSamtools  but i don know what i can do there...

ADD REPLYlink written 5.0 years ago by A3.7k

RSamtools is a module for the R scripting language.

As for Galaxy, you don't have to install anything locally. Go to and click on the "Get Data" link on the left-hand sidebar. When it expands, click "Upload File" and upload your BAM.

After that, search the tool list on the left-hand sidebar for "bedtools". Then in the list that pops up click "Create a histogram of genome coverage". Bada-bing.

ADD REPLYlink written 5.0 years ago by Dan D7.1k

thank you Dan, you are always helpful...

ADD REPLYlink written 5.0 years ago by A3.7k
gravatar for Dan D
5.0 years ago by
Dan D7.1k
Dan D7.1k wrote:

Indeed bedtools is intended to be used in an OSX/Linux environment. However there's an R implementation called RSamtools which would give you equivalent functionality in a Windows environment. 

You could also run the data through Galaxy if you have the bandwidth to push your BAM up to it.

ADD COMMENTlink written 5.0 years ago by Dan D7.1k
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