Using CTCF chip-exo without input

[re2srm]

Hello,

I have CTCF chip-exo data and unlike chip-seq it doesnt have an input sample. I have generated the bigwig file but cannot run ctcf_norm.sh to normalize it as I dont have an input sample. Can I use the bigwig file directly without normalizing it?

I do have a chip-seq input sample from the same cell line but I am not sure if I should use that for normalizing the chip-exo data.

Thanks

[tanjimin]

The ChIP-seq has to be normalized with log2fc w.r.t. input. You can use the input sample from the same cell line as input data and see how it goes.

[re2srm]

Thanks. Will try that.

[re2srm]

I had another question about the atac-seq input files. I used the seqnslide atac pipeline to generate the atac bigwig file for my cell line. But I just noticed that the atac_pipeline.sh in the preprocessing folder subsamples 40M reads before running the pipeline. Is it a required step? My atac sample actually has less than 40M reads.

[tanjimin]

Yes 40 million subsample is a required normalization step.

[re2srm]

Hi, another question about the ctcf input data. When I normalize my ctcf against input, there are regions where the log2fc w.r.t input is negative. I also did this for some published ctcf data and got the same result. Were your normalized bigwig files similar? Or should I remove the negative values from the bigwig before using them as input. Thanks