Question: Overlapping Bedgraph - Microarray ChIP to BigWig for Clustering analysis
gravatar for Hushus
12 months ago by
Hushus 20
Hushus 20 wrote:

Good afternoon everyone,

I've been playing around with publicly available ChIP-seq datasets and have been clustering regions, producing heatmaps, and all that fun stuff. Now, my data analysis hinges on a set of ChIP-chip (on microarray) data and Im having trouble interpreting the data deposited to convert it to a BigWig file to continue my analysis. Im not looking for peak calling, im looking to make more heatmaps using all the other data I have in BigWig files so far.

I have semi-processed microarray data (after feature extraction) which gives me the genomic coordinates along with the LogRatio (gProcessed/rProcessed) along with all the other columns. From my understanding, you can take the LogRatio values, use them as scores and create a Bedgraph file. I'm aware that HOMER takes bedgraph files but I want to use all the other data I have in BigWig Files.

Next step is to convert the Bedgraph into BigWig but there are overlapping regions. I've seen some scripts which deal with this problem but I am a novice in computation and would like an easier, GUI-based solution (like using the Galaxy project for example).

Questions: 0) Is it correct to take the LogRatio and use it as scores? 1) Is there a simpler way to take the feature extraction file and make a BigWig out of it? 2) If not, is there a way to smooth out the overlapping regions by averaging the values out?

Thank you

ADD COMMENTlink written 12 months ago by Hushus 20
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