Is there something wrong with my GTF file that I am trying to use to analyze repeats in HOMER? How do I tell?

Question

[baunruh]

Hello!

I am trying to use the program HOMER to analyze repeats and get gene expression in TPM, I am using custom GTF files downloaded from https://miso.readthedocs.io/en/fastmiso/annotation.html.

Everytime I run the program with these GTF files it gives me an error output saying 0 of 0 repeats counted...

this is my input command:

analyzeRepeats.pl mm9ALE.gtf mm9 -rpkm -d /mytag/ > /rpkm_my.out

The error is in the GTF file but if I use a GTF file from the UCSC browser window it works just fine. I want to use the GTF for the Alternative Last Exon instead from the website I mentioned.

[Kevin Blighe]

The error that you report may be related to the fact that it cannot parse the GFF3 file from MISO. You should convert this to GTF for HOMER with:

gffread mm9/ALE.mm9.gff3 -T -o ALE.mm9.gtf

gffread comes shipped with Cufflinks / StringTie, if you happen to have either of those installed.

Be also aware that the annotations used by MISO may neither be compatible with your data.