Closed mmpust closed 10 months ago
Hi @mmpust it looks like the transcript names are not unqiue, which could cause a problem? can you make the transcript names unique, for example by adding a running index or something like that?
I also meet this problem when I used the gtf file to do annotation, how to solve it? Thank you very much!
library(proActiv)
## From GTF file path
gtf.file <- '/mnt/ruiyanhou/nfs_share2/RNA_seq_organ_species/chicken/ref_files/galGal4.ensGene.gtf'
promoterAnnotation.gencode.v34.subset <- preparePromoterAnnotation(file = gtf.file,
species = 'Gallus_gallus')
The error looks like this
I haven't had time to look into this yet in detail, but could you first try subsetting your gtf to standard chromosomes:
awk -F'\t' '$1 ~ /^chr([0-9]+|M)$/' galGal4.ensGene.gtf > galGal4.ensGene.filtered.gtf
then create the transcript database and build promoter annotations?
library(GenomicFeatures)
library(proActiv)
path <- 'galGal4.ensGene.filtered.gtf'
txdb <- makeTxDbFromGFF(path)
anno <- preparePromoterAnnotation(txdb = txdb, species = 'galGal')
Thank you for your quick response! It works according to your suggestion! Thank you very much!
But I meet another problem in the new issue, could you help me? Thank you!
Hi, I am running into the following error message:
Any ideas what I can do about it? Thanks in advance!