Hello everyone, I have BigWig files from a ChIP-Seq experiment. I need to find the differences between the two tissues. How can I find the information like differentially changed genes with p-values or fold changes of peaks between two tissues? Maybe a desktop app to visualize my files can work.
I am sorry my question is really simple maybe but I am in a rush and I only have BigWig files. Also I can convert BigWig files to BedGraph files.
Thank you.
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written
by
hkarakurt
1 answer
If you want p-values you should go back to the BAM files, particularly if you don't know exactly how the bigWig files were made. Then the standard procedure would be to either call differential peaks between the samples (e.g., with MACS) or use something like diffBind, if you want to compare signal in peaks between the samples.
If you're OK without p-values then you can visualize the files with deepTools (computeMatrix and plotHeatmap). Presumably make a k-means clustered heatmap would be useful.
BigWig files can't contain gene information, you'll need a BED or GTF file with that.
Hi, You can open the bigwig file with the .fasta file and .gff file on igv. That way you can compare the peaks across different conditions.
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