search

getzlab / rnaseqc

Fast, efficient RNA-Seq metrics for quality control and process optimization
Other
150 stars 19 forks source link

Error when running rnaseqc with non-standard gtf annotation file #75

Closed magmir71 closed 2 years ago

magmir71 commented 2 years ago

Hi!

I have bam files, which were produced with an annotation file, in which chromosome identifies are 1,2,..., X, Y, M, so, not chr1, chr2,..., as in the GENCODE annotation. I changed the identifiers in the GENCODE annotation file accordingly, then ran collapse_annotation.py on it. No problems occured, a correct collapsed file was produced. But then, when I run rnaseqc, I get the error:

Failed to parse the GTF: Exon missing exon_id and gene_id fields: 1 HAVANA exon 11869 12227 . + . "gene_id ""ENSG00000223972.4""; transcript_id ""ENSG00000223972.4""; gene_type ""pseudogene""; gene_status ""KNOWN""; gene_name ""DDX11L1""; transcript_type ""pseudogene""; transcript_status ""KNOWN""; transcript_name ""DDX11L1""; level 2; havana_gene ""OTTHUMG00000000961.2"";" exon_id "ENSG00000223972.4_1; exon_number 1";

With usual annotation file, rnaseqc runs correctly. I used rnaseqc.v2.4.2.linux

Best, Aleksei

magmir71 commented 2 years ago

I guess, my modification of annotation file was not correct, because with Ensemble annotation file, which also has 1,2,..., X, Y chromosome identifiers, everything worked. Sorry