Hi, I’m trying to carry out a DiffBind operation with peak files (in bed format) generated elsewhere. When selecting my input files and parameters, the default setting for Score Column for a narrowPeak file is column number 8. In my narrowPeak files, column 8 corresponds to the -log10(pvalue). Is this what the score refers to, or should I be changing the column number to correspond to another column, like abs_summit or fold_enrichment? I should note that none of the columns in the narrowPeak file are actually called ‘score’. Thanks in advance!
Hi @alexbisias
Usually, yes, the p-value is what is used for “score” when calculating the FDR.
The file format for narrowPeak datasets is here: Genome Browser FAQ
You’ll notice the first few columns are similar to BED format, which has a score metric in the 5th column, but what that score represents differs between the two plus narrowPeak has two more summary attributes.
Resources
-
Diffbind
- Usage from the tool form’s help section in Galaxy:
https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf - Bioconductor author Q&A forum: https://support.bioconductor.org/post/search/?query=diffbind
- Usage from the tool form’s help section in Galaxy:
-
MACS2
- See the README and ISSUES to start with https://github.com/macs3-project/MACS
- Google Group author Q&A: https://groups.google.com/g/macs-announcement/
-
Tutorials
- https://training.galaxyproject.org/training-material/search?query=ChIP-seq
- https://training.galaxyproject.org/training-material/search?query=macs2
- And, the author resources have more examples
The GTN and Bioconductor groups will be hosting a training later this month. Please consider joining for direct expertise help from the original tool authors and scientists from both communities 
Smörgåsbord 3: A week of Free, Online, Galaxy Training supported by the Global Galaxy Training Community
Hi @jennaj, thank you for the clarifications, and for highlighting the course, that’s very helpful!
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