ys3508
commented
2 weeks ago To add more background to my question. For the purpose of footprinting, rather than identifying TF motifs using all peaks, I want to focus specifically on differential peaks identified through differential analysis (using DiffBind). To achieve this, I used bedtools intersect to extract differential peaks from the alignment BAM files (let's call these the DE-only BAM files for clarity). I set a minimum overlap of 10%.
Initially, I used the DE-only BAM files for peak calling with MACS2. However, when I checked the resulting narrowPeak files, I noticed they had extremely high scores, q-values, and p-values, and the bias model training failed. To address this, I used bedtools intersect again, this time to extract differential peaks from the narrowPeak files (which were generated from peak calling on the original alignment BAM files), creating what I'll refer to as the DE-only narrowPeak files.
Here is the workflow:
Here's your text with some adjustments for clarity:
Based on this workflow, I have a few possible reasons for the issues encountered:
The DE-only narrowPeak files and the non-peak regions required for bias model training might be insufficient, leading to an empty data frame. The DE-only narrowPeak files are not directly generated from peak calling on the DE-only BAM files. Instead, I manually extracted the DE peaks from the original narrowPeak files. As a result, the DE-only narrowPeak files might not correspond accurately with the DE-only BAM files. Below is a table showing the number of peaks in the input files for both the DE-only BAM files and the DE-only narrowPeak files:
akundaje
I am working on ATAC-seq mice data and have developed a function to run bias model training across all folds and comparison groups. While testing the function with fold 1 and the group fed_vs_fasted_0hr, I encountered the following error (I attach the details in the end): IndexError: list index out of range
Debugging Steps: I checked the number of unique chromosomes in the input BAM file, narrowPeak files, and the background file (non-peak regions):
Input BAM file:
narrowPeak files:
Background file (non-peak regions):
fold_1.json: { "test": [ "chr1", "chr2", "chr3", "chr4" ], "valid": [ "chr5", "chr6", "chr7", "chr8" ], "train": [ "chrX", "chr10", "chr14", "chr9", "chr11", "chr13", "chr12", "chr15", "chr16", "chr17", "chrY", "chr18", "chr19" ] } Could you please help identify the cause of this error and suggest a possible solution?
Thank you!
Error: