Question: Deeptools for ChIP-Seq
0
gravatar for yugen30
15 months ago by
yugen3010
yugen3010 wrote:

Hello,

I am new to deeptools and have referred to this post Y axis PlotHeatMap Deeptools. I am still not clear on what the Y axis represents in my case enter image description here

The figure shows 2 ChIP-Seq replicates (1_normalized and 2_normalized); these are generated using bamCompare. Also, is there a way to combine my ChIP-seq replicates in deeptools?

heatmap chip-seq deeptools • 998 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by yugen3010

Your image is broken and should be embedded directly.

Well, what files did you feed into bamCompare? Both of your replicates or each replicate individually against a control (IGG, input, etc)? What's in your bed files being fed to plotHeatMap?

You can use samtools to merge bam files, though it's usually best to show replicates individually when possible.

ADD REPLYlink written 15 months ago by jared.andrews076.4k

Okay. Thank you for your replies! I fed in the bam files - each replicate against its control - into bamCompare. The bigwig files were then used in computeMatrix and finally the matrix file was used to generate the heatmap. How can I obtain the top genes with the peaks in/ near the TSS from this?

ADD REPLYlink modified 15 months ago • written 15 months ago by yugen3010

Hi Yugen30 were you able to figure out what the Y-axis meant?

ADD REPLYlink written 9 months ago by rohitsatyam102170

were you able to figure out what the Y-axis meant?

ADD REPLYlink written 5 weeks ago by yiren0
1
gravatar for ATpoint
15 months ago by
ATpoint36k
Germany
ATpoint36k wrote:

The y-axis is whatever value was used to generate the bigwig files. Probably a kind of normalized read count, but it technically can be any numeric value. bamCompare in deeptools can combine replicates.

ADD COMMENTlink written 15 months ago by ATpoint36k
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