A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Dear chipseq dev team, is it possible to not provide the input/control samples for the future? In practice, people might re-use the previously analysed input data for downstream analysis. Thus not every time input samples are sequenced/available. Thanks in advance!

you mean to provide directly the aligned reads (bam files) as input?

Yes, that’s one possibility. However, since MACS3 can perform peak calling without input/control samples, could we consider making them optional instead?

Just saw this topic has been discussed several times before. People suggested to use other pipelines such as nf-core/atacseq or cutandrun to get around this: (<https://github.com/nf-core/chipseq/issues/384>)

Yes, as a best practices pipeline we have been always reluctant to include this option in the <#CFP55NZ5G|> pipeline