HI everyone.

Which packages in R do you recommend to use for operations on the bedgraph files eg conversion from bedgraph into bigwig, union, etc...

Thanks,

Bogdan

Bioconductor's rtracklayer can import and export bed, bedgraph and bigwig files. It handles them as GRanges objects - they contain chromosome, range (start, end), strand and any necessary metadata (e.g. score). Bioconductor pacakge GRanges allows for manipulation of these objects, including a union. The combination of the two should do the trick.