I run this cmd
./stringtie G1_sorted.bam -B -o G1.gtf -G Triticum_aestivum.IWGSC.42.gtf -p 4 -C G1.refs.gtf -A G1.abund.tab
-WARNING: no reference transcripts were found for the genomic sequences where reads were mapped! Please make sure the -G annotation file uses the same naming convention for the genome sequences.
How can I resolve it?
I have downloaded both (GTF and Refernce Genome)files from Ensemble. Can you confirm me that whether theu have same chromosomes naming? So that i can perform my mapping task of GTF File with Reference Genome which usually i remain fail to do due to difference in chromosomes naming. Here The Reference genome file is shown as:
>1A dna:chromosome chromosome:IWGSC:1A:1:594102056:1 REF CTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCCTAACCCTAAACCCTAACCAAAAC
Where as The annotation file (gtf file ) is as
#!genome-build IWGSC #!genome-version IWGSC #!genome-date 2018-07 #!genome-build-accession GCA_900519105.1 3B IWGSC gene 212892 214491 . - . gene_id "TraesCS3B02G000100"; gene_source "IWGSC"; gene_biotype "protein_coding"; 3B IWGSC transcript 212892 214491 . - . gene_id "TraesCS3B02G000100"; transcript_id "TraesCS3B02G000100.1"; gene_source "IWGSC"; gene_biotype "protein_coding"; transcript_source "IWGSC"; transcript_biotype "protein_coding";
Can it be confirmend that these both files are same ? If not same with chromosome naming convention , then please suggest me how can I change it ?