Question: is it possible to merge bigwig files? about libbigwig

[dpryan79]

I don't have any specific merge functions in libBigWig, you would iterate over the intervals in two or more files and merge them as you go.

[romgrk]

So overall, I'd need to get the list of chroms for both files, merge them, iterate all intervals with bwOverlappingIntervalsIterator, and merge those intervals? And how would I merge those intervals?

Sorry for bothering, I'm a noob in regards to genomics data so I'm not even sure what those intervals represent :/

[cmdcolin]

You might look into https://github.com/Ensembl/WiggleTools

[romgrk]

Thanks @cmdcolin! But I went a different way, I forked kent tools and re-used the code of bigWigMerge to create bigWigMergePlus: a tool to directly merge bigWig files into another bigWig. It contains also a few more features that were needed in the case of our project, such as outputting the standard deviation. Release is here: https://github.com/c3g/kent/releases/tag/bigWigMergePlus_2.0.0

[nsheff]

FYI I think this is also basically what bigWigCat does

https://github.com/ENCODE-DCC/kentUtils/tree/master/src/utils/bigWigCat

[dpryan79]

I think bigWigCat is meant for when the intervals in the files don't overlap. I'd suggest sticking to wiggletools, which uses this library.