converting bedgraph to bigwig by not using ucsc tools

Question

[Bogdan]

Dear all,

Are there any other software that you'd recommend to convert directly bedgraph into bigwig, beside using UCSCtools (bedGraphToBigWig) ? Thank you,

Bogdan

Answer 1

[cmdcolin]

I'm not sure of the exact function to do this but libBigWig may be one non-ucsc example of this https://github.com/dpryan79/libBigWig which has python interfaces https://github.com/deeptools/pyBigWig and https://github.com/brentp/bw-python

I would also be curious in the answer for this, I had a user saying that creating merging bigwigs from multiple chromosomes was prohibitively memory intensive for them

[ATpoint]

I generally go the path of bigwig -> BigWigTobedGraph-> bedtools unionbedg (or custom awk-fu) -> bedGraphToBigWig for that, which essentially has no memory footprint, though all that file conversion-fu is a bit of an anticlimax.

Answer 2

[ATpoint]

The bg2bw utility in https://github.com/cancerit/cgpBigWig can do that, but it will only compile on Linux iirc based on how they coded up the compilation instructions. It builds on the pyBigWig library linked by @cmdcolin

[Bogdan]

I have tried to install it on Mac, and I am getting an error :

+ INIT_DIR=/Users/tanasab/Desktop/SOFTWARE/cgpBigWig/cgpBigWig
++ grep -c '^processor' /proc/cpuinfo
grep: puinfo: No such file or directory
+ CPU=

How shall I setup the file "cpuinfo" ? Thanks !

[ATpoint]

As I said, it compiles on Linux, not Mac. The way they coded up the compilation instructions are not compatible with macOS. /proc/cpuinfo does not exist on macOS.

Answer 3

[Bogdan]

Thank you everyone. I was asking because sometimes the ucsc tools perform a conversion bedgraph > bigwig that is not properly read in IGV. The error that I have gotten is :

Error loading /Users/tanasab/Downloads/GSE103543_AR16_H3K4me3_Corrected_HMD.bigwig.gz: Error reading BBFile header for: /Users/tanasab/Downloads/GSE103543_AR16_H3K4me3_Corrected_HMD.bigwig.gz

[ATpoint]

I am reasonable sure gzipping a bigwig breaks any downstream tool. Decompress and repeat. It anyway makes limited sense as bigwig is already a compressed format.

[Bogdan]

Thanks. I can upload the bigwig files that are not griped.