Entering edit mode
7.2 years ago
moxu
▴
510
Sorry for the simple question, but what's the best way to convert bigWig to bigBed?
One can do the following:
bigWigToWig wig2bed bedToBigBed
which looks convoluted and I am not sure if this is the (best) way to do it.
Thank you!
That's probably the best way to do it. However, I wonder why you want to do that. bigBed is tweaked weird version of bigWig that needs more space. I would expect that anything supporting bigBed also supports bigWig.
Well, here is the bigWigCorrelate help information:
It requires "bigBed" for the "restrict" option.
Makes sense. Just be sure that the resulting bigBed file has useful regions. If your bigWig file is base-level resolution or something like that then the resulting bigBed file probably won't be useful.
BTW, an alternative would be to use multiBigwigSummary from deepTools, followed by plotCorrelation (also from deepTools).
The step of bedToBigBed had the following error:
a.bed looks like the following:
Anything wrong?
Thank you.
I'm not sure it can take floats, either cut off that column or replace it with a
.
or some random integer.You are right, after truncating .000000, it finished without a problem. It's odd, though, because the bed file was generated by wig2bed. Thanks.
¯\ _ (ツ)_/¯