Question: How to extrach gene names and peaks from BedGraph or BigWig files
0
gravatar for hkarakurt
10 months ago by
hkarakurt30
hkarakurt30 wrote:

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.

bigwig chip-seq bedgraph peak • 529 views
ADD COMMENTlink modified 10 months ago by Devon Ryan88k • written 10 months ago by hkarakurt30
1
gravatar for Devon Ryan
10 months ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

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.

ADD COMMENTlink written 10 months ago by Devon Ryan88k

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.

ADD REPLYlink written 10 months ago by hkarakurt30

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

ADD REPLYlink written 10 months ago by Devon Ryan88k

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

ADD REPLYlink written 10 months ago by hkarakurt30
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