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deeptools / deepTools

Tools to process and analyze deep sequencing data.
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Use CWig instead of Bigwig #97

Closed lelouar closed 8 years ago

lelouar commented 9 years ago

The format uses on average one-third of the size of existing bigWig files and improves random query speed up to 100 times. (CWig: compressed representation of Wiggle/BedGraph format)

You can also use cython to enhance performances.

fidelram commented 9 years ago

Thanks for letting us know about the CWig format. I will see what I can do.

lelouar commented 8 years ago

A new format for compression of wig is come out : Wang, Zhiying, Tsachy Weissman, and Olgica Milenkovic. “smallWig: Parallel Compression of RNA-Seq WIG Files.” Bioinformatics, September 30, 2015, btv561. doi:10.1093/bioinformatics/btv561.

they argue that this format is (or seems to be) better than bigWig and Cwig.

dpryan79 commented 8 years ago

I would suggest that we close this, since there's no point in making Cwig or smallWig files when IGV/et al. don't support them.