Can we do chip seq analysis using nextflow without input sample?

[autumnfe79]

Description of feature

I'm trying to do chipseq analysis in public dataset.

But, there is no input sample in geo. In that case, can we use nextflow for analyzing chip seq data?

[JoseEspinosa]

Not sure to understand your question, you will need to download the data and create the suitable samplesheet following the documentation here.

[Nicobouch]

The possible meaning is that "input" DNA was not sequenced; only ChIP DNA is available. Can the pipeline be run without input sequences? I have the same question. Thanks.

[Kevin-Brockers]

I think there was a discussion on slack a while ago.

Current Encode standards discourage to perform ChIP-Seq experiments without controls, see: https://www.encodeproject.org/chip-seq/transcription_factor/#standards. Therefore, using the ATAC-Seq pipeline might be a good workaround for older publicly available ChIP-Seq data, where matching controls (inputs) are missing @JoseEspinosa could you confirm / what do you think?