Hi, I am analyzing RNA-seq data for alternative splicing analysis and used for this reason RefSeq human genome as reference (hg38.p14). I have a list of alternatively spliced exons significant for my conditions obtained using DEXSeq.

I want to select only exons that are located in the CDS and not in the UTR regions to obtain a list of events that could be related to some protein conformational change. To do so I tried to use methods that are typically used for chIP-seq analysis.

I used annotatePeaks.pl from homer software, however both when using the default annotation and when giving a custom GTF file the result table contains only NAs in the columns where the annotations should be.

I ran annotatePeaks as:

annotatePeaks.pl exon_intervals.txt hg38 -gtf hg38.ncbiRefSeq.gtf > annotated_exon_intervals.txt

And this is the head of the resulting table:

PeakID (cmd=annotatePeaks.pl ./data/caco2_rnaseq/DEXSeq_refseq/exon_intervals.bed hg38 -gtf ./rawdata/genomes/human/refseq/hg38.ncbiRefSeq.gtf) Chr Start   End Strand  Peak Score  Focus Ratio/Region Size Annotation  Detailed Annotation Distance to TSS Nearest PromoterID  Entrez ID   Nearest Unigene Nearest Refseq  Nearest Ensembl Gene Name   Gene Alias  Gene Description    Gene Type
F10:004 13  113139357   113139470   +   +   NA  NA  NA  NA  NA                              
LOC105373422:003    02  9950705 9950853 +   -   NA  NA  NA  NA  NA                              
CEP72:021   05  656928  657088  +   +   NA  NA  NA  NA  NA                              
HTATSF1:009 23  136509091   136509180   +   +   NA  NA  NA  NA  NA                              
ZNF106:018  15  42446589    42446658    +   -   NA  NA  NA  NA  NA

...

I tried to use as input both the bed format and the homer input format but the result does not change. I am not using the proper type of data which could affect the anlaysis. I am open to solution but also new ways of annotation exons to CDS/UTR.

Thank you,
Alessia