bamcompare input corrected chipseq file

[girdhar3]

Hi there, I am using bamCompare to create input_corrected chip file. Is that what you would suggest to use as input corrected bam file? bamCompare -b1 chip_sample -b2 input_control_bam -of "bigwig" -o chip_input_corrected.bigwig

[thouis]

@jnasser3 - Can you answer this?

[mayasheth]

Just circling back to this issue: technically bigwig files are supported as an H3K27ac file format, including input-corrected bigwigs. However, we have only tested and benchmarked the performance/validity of ABC using non-input-corrected H3K27ac files, as the total signal at each candidate element contributes to activity, not just the "sample-specific" signal.

If your goal is to find regulatory interactions that are specific to your sample compared to the complete input, I would recommend running ABC on the (non-corrected) sample inputs and the combined inputs, and comparing the two at the predictions stage.