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I'm trying to run differential loop analysis using the script Imp_Scripts/DiffAnalysisHiChIP.r on a 2-conditions but only 1 replicate per condition data, without ChIP bam files.
However I got 0 significant loops identified. By checking the all differential loop results, I found all tested loops FDR results are 1. Do you have any suggestions why?
Here's my code for running the differential analysis.
The loops I used are from upstream results: FitHiChIP_Peak2ALL_b5000_L20000_U2000000/P2PBckgr_0/Coverage_Bias/FitHiC_BiasCorr/FitHiChIP.interactions_FitHiC.bed
I'm wondering why the FDRs I got are all 1? Is there anything I need to change in the code? I appreciate your suggestions!
Thank you!
The text was updated successfully, but these errors were encountered:
Hi @helenhuangmath
It may be due to the issue that HiChIP counts between different conditions may not be drastically different. Could you please check the output file "Loops_EdgeR_Default.bed" (containing complete edgeR results) and specifically the entries with p-value < 1e-5?
Hello,
I'm trying to run differential loop analysis using the script Imp_Scripts/DiffAnalysisHiChIP.r on a 2-conditions but only 1 replicate per condition data, without ChIP bam files.
However I got 0 significant loops identified. By checking the all differential loop results, I found all tested loops FDR results are 1. Do you have any suggestions why?
Here's my code for running the differential analysis.
The loops I used are from upstream results:
FitHiChIP_Peak2ALL_b5000_L20000_U2000000/P2PBckgr_0/Coverage_Bias/FitHiC_BiasCorr/FitHiChIP.interactions_FitHiC.bed
I'm wondering why the FDRs I got are all 1? Is there anything I need to change in the code? I appreciate your suggestions!
Thank you!
The text was updated successfully, but these errors were encountered: