tools to get the coverage

Question

[Sara]

I have tried to get the coverage of the reads per base. to do so I used samtools bedcov and bedtools genomecov. I got almost different coverages. do you know what the difference is between these 2 tools?

[Sej Modha]

bedtools genomecov is explained in depth here: http://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html

[ATpoint]

When posting these kind of questions, please provide:

• the exact command line for every tool
• an example of the input data
• an example of the output data

Without these information, we cannot help you at all, as these tools have a plethora of options, not even talking about all the different kinds of data one can feed in.