HOMER annotatePeaks.pl with GFF. How to specify a feature?

Question

[callapus]

HI, Having an issue running annotatePeaks.pl with a GFF annotation file (working in a non-standard organism and this is all I have available to me). Unfortunately in my GFF file exons are actually marked as CDS so annotatePeaks is not able to annotate my called peaks. The output:

Features that will be considered: exon

0 lines contained useful feature information This seem very low - consider specifying specific features (i.e. 'exon', 'transcript', etc.) or use "-keepAll"

My problem is I can't figure out how to specify the feature 'CDS' in my GFF. It does seem like it's possible to specify features however. Ive gone back and changed CDS to exon in my GFF file and annotatePeaks runs fine but would still find this really usefull if anyone knows how to do it! Thanks in advance!! C

Answer 1

[Qiongyi]

You may be able to use the option of "-keepAll" or "-features" as I saw the source code of parseGTF.pl offer these options. However, exon is the essential feature that GTF/GFF file should contain, which is used to determine the TSS and TES, etc. It is better that you use a proper GTF/GFF file for the annotation. Simply replacing CDS to exon is not a correct way (CDS != exon).