Extracting list of target genes from ChIP-seq bigwig file

Question

[jennifer.conrad84]

I am reading a publication where the authors performed ChIP-seq on a specific TF. Their data was deposited on NCBI in bigwig format. I would like to extract the final list of target genes. Is this possible using the bigwig file or am I going to have to go back to the fastq files and follow their pipeline? I do plenty of RNAseq analysis but haven't done ChIP-seq analysis in maybe 10yrs and I don't remember how I would go about this.

[hukai916]

You can use ChIPpeakAnno::annotatePeakInBatch() to annotate the peak file to the nearest genes.

[ATpoint]

A bigwig file is a plain pileup of the reads, it is nothing you can use with this function.

Answer 1

[ATpoint]

I personally would first check whether the data is part of the ReMap2022 database which would allow download of a peak BED file: https://remap2022.univ-amu.fr/

If not then I would start from the raw data. You do not know how the deposited bigwigs were created and the "gold standard" peak callers such as macs typically start from BAM files, not bigwigs. Custom workarounds are probably error-prone. You can either use existing pipelines for ChIP-seq such as nf-core or snakepipes or run something locally. It comes down to alignment, some filtering (primary alignments, main chromosomes, MAPQ>20 (for example), non-duplicate reads) and then feed this into a peak caller such as macs2.