Hi everybody! I am using RNA-Seq protocol for identifying differentially expressed gene in RNASEQ data of 6 wheat varieties. I am following this protocol https://www.nature.com/articles/nprot.2016.095. My Reference genome source is as under. I downloaded the assembled sequences from ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/519/105/GCA_900519105.1_iwgsc_refseqv1.0. I Downloaded GCA_900519105.1_iwgsc_refseqv1.0_genomic.fna.gz file. This contains the FASTA formatted sequences of the chromosomes. here as my GTF file source is ftp://ftp.ensemblgenomes.org/pub/release-42/plants/gtf/triticum_aestivu After hisat step to get the Assembled transcripts I am taking sorted Bam files as input to stringTie. I am using following command ./stringtie G1_sorted.bam -G Triticum_aestivum.IWGSC.42.gtf -l G1-Label -o G1_ST.gtf -p 15 and the following error appear

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 Can someone please suggest a solution.