How Would One Correlate A Wig/Bedgraph File With A Bigwig File?

Question

[hlsz.laszlo]

Hi all,

I've made several correlation with my ChIP-seq data (hg19) wig files (variable step) with ENCODE .bigWig files with wigCorrelate software. It makes the correlation, is this correalation valid?

Can you correlate wig/bedGraph with bigWig? Which is the best way to create wig files?

Thank you for your answer. L

Answer 1

[Björn]

Hi Laszlo,

I don't fully understand your problem. You can correlate nearly every format which each other if your tools are capable of it. I think you need to give a little bit more information what you are trying. In the meantime you can have a look at deepTools. Is has two tools to create bigwigs from your bam files and a tool called bigwigCompare. Maybe these tools are useful for you.

Cheers,

Bjoern

[hlsz.laszlo]

Thanks Bjoern,

I read that wigCorrelate, finds the overlapping features between two wig and calculate base-to-base Pearson's Coefficient. When I correlated the data, some correlation was way too low then expected. So, now, I want create 1000 bp windowed wigs from bam files with igvtools count and then correlate them. Is there a way to create 1000 bp windowed wig from bigWig? I will check out deepTools.

L