Bedgraph And Bigwig Files From Multiple Bams

Question

[andrew.j.skelton73]

Is it possible to combine multiple BAM files to create a consensus Bedgraph file?

[Pierre Lindenbaum]

what's the 'value' in the bedgraph ? the depth ?

[Devon Ryan]

Depends on the nature of the data that you're getting from the bedGraph files. In general I would suspect that'd work, but I'm sure there are edge cases where it wouldn't (e.g. when using bedGraph to represent present/absent features, since calling those might be affected by merging the BAM files).

Answer 1

[Ryan Dale]

If you have separate bedGraph files, you could convert to bigWig and then use the bigWigMerge utility from UCSC.