How to generate .cov files using .bam files

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Hello,
How to generate .cov files in the galaxy with the help of .bam files. Is it possible using bedtools genome coverage tool?

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Hi – Sorry this question got missed earlier.

Do you want to create an alignment “coverage” summary of your data? This is usually represented in wiggle or bigwig (compressed “wiggle” format) and sometimes bedgraph. The Bedtools, Deeptools, and RSeQC tools can be used for that. Search the tool panel with the keyword “coverage” to find the tools, if working at a public server. The same tools are available in the ToolShed to install into your own Galaxy (cloud/docker/local).

If instead, you want a “covariate” type of output, what kind of analysis are you doing? ChIP peaks, SNP variation, or ? What downstream tool are you trying to generate input for (if any)?

Thanks!