Control data for chip-seq analysis of SRX681547, SRX681548 data

Question

[gskbioinfo143]

Dear all,

im working on chip-seq analysis of SRX681547, SRX681548 data using galaxy suite for peak calling, motif finding and differential expression analysis. i have query regarding control data set while doing MACS analysis. for this dataset can we do MACS analysis without control data?. if not then what has to be used as control data.

Need Help.

Hope to hear from you

Thank you

Answer 1

[Satyajeet Khare]

You can perform MACS peak calling without control. But since you are referring to a published dataset, you can refer to the publication or contact the authors for their analysis pipeline. I am not sure how you will perform differential expression analysis with MedIP data.

Answer 2

[Devon Ryan]

MACs won't be very useful, you're not looking for peaks, you're looking in differences in methylation, which generally looks more like a dip in the signal instead. You're better off using something like batman than either MACs or homer (what they did in the paper that created those samples).

[gskbioinfo143]

Hi im actually looking for unique enriched peaks with p values from treatment (SRX681547) and control (SRX681548) samples using peak calling. I have used MACS in galaxy to get peaks (.bed) from both samples then i inputted into SICER to get enriched regions but analysis fails.

Is there any tool which gives unique enriched peaks taking treatment and control samples .bed peak files

need help thank you

[Satyajeet Khare]

Bed intersect should give you unique peaks in treatment unique peaks in control, overlapping peaks in treatment and control, or all peaks in both treatment and control.

[gskbioinfo143]

Hi,

in MACS output files, the peak interval file has -10*log10(pvalue) values for each peaks.

know how to get the original pvalues for each peak data. In result files it gave calculated value using ablove formula. shall i reverse the formula to get that pvalue?

thank you

[gskbioinfo143]

Hi Sir,

in MACS output files, the peak interval file has -10*log10(pvalue) values for each peaks.

know how to get the original pvalues for each peak data. In result files it gave calculated value using ablove formula. shall i reverse the formula to get that pvalue?

thank you