Strand information when doing peak annotation with HOMER
1
5
Entering edit mode
4.7 years ago
jiab ▴ 60

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

HOMER annotation ngs • 3.4k views
ADD COMMENT
0
Entering edit mode

(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

ADD REPLY
1
Entering edit mode
4.7 years ago

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)
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 1734 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6