using GenomeCoverageBed tool

Question

[zizigolu]

Guys,

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.

Answer 1

[Dan D]

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.

[zizigolu]

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.

[Dan D]

RSamtools is a module for the R scripting language.

As for Galaxy, you don't have to install anything locally. Go to usegalaxy.org 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.

[zizigolu]

Thank you Dan, you are always helpful...