Strand information when doing peak annotation with HOMER

Question

[jiab]

As far as I can tell (by running tests manually), annotatePeaks.pl in the HOMER package [1] ignores strand information when searching the Transcription Start Site (TSS) nearest to each peak. After a close inspection of the various settings available, I couldn't identify one which changes this behaviour.

This was unexpected for two reasons:

• HOMER actually requires input to have a Strand column [2]
• The data from some NGS technologies are directional (e.g CAGE), so strand information should be used when assigning the peaks to transcript/gene models

Could someone please comment if I'm missing something here?

Thanks

[1] http://homer.ucsd.edu

[2] http://homer.ucsd.edu/homer/ngs/annotation.html

[jiab]

(A couple more things to bare in mind when searching for an annotation tool:)

PeakAnnotator [1] also ignores strand information (accordingly to its paper [2]) and consider this post [3] for strand-related issues with the ChIPpeakAnno [4] R packages.

[1] http://www.ebi.ac.uk/research/bertone/software

[2] https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-415

[3] http://guangchuangyu.github.io/2014/01/bug-of-r-package-chippeakanno/

[4] https://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html

Answer 1

[Lars Juhl Jensen]

According to the documentation on the second page that you link to yourself, the behavior depends on the -strand argument:

-strand <+|-|both> (Count tags on specific strands relative to peak, default: both)

[jiab]

Well, that still ignores per peak strand information actually contained in the input. But it means I have the option of splitting the input based on strand and running HOMER twice with the appropriate -strand setting.