How to extrach gene names and peaks from BedGraph or BigWig files

Question

[hkarakurt]

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.

Answer 1

[Devon Ryan]

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.

[hkarakurt]

I am using deepTools now (on Galaxy Server) and compare the BigWig files then my plan is to visualize them in IGV but the problem is my BigWig files does not include any gene information.

I am not sure what should I do now.

[Devon Ryan]

BigWig files can't contain gene information, you'll need a BED or GTF file with that.

[hkarakurt]

Thank you for your help. I think I should start from raw data to have better result.

[mankadeep2]

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.