text: user4194: 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
  
  Error is:
  -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?
  Update:
  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 ?
  
  user1135: This seems to be a common problem. As @llrs pointed out, Ensembl, UCSC(genome browser and associated data) and NCBI records are not directly interchangeable. The ambiguity refers to annotation as well as the reference genome. The reference genome is identical, except for the chromosome naming convention, meaning a reference from Ensembl might not contain CHR prefix, whereas it will be present in one downloaded from UCSC.
  To prevent such conflicts in downstream tools, it is good to stick to the reference and annotation from the same repository throughout the analysis and map the genes to gene names or whatever towards the end of the investigation. 
  You can download all the associated data for T. aestivum which I beleive is the organism you want to study from Ensembl plants FTP download. 
  
original_text: 4194: <p>I run this cmd </p>
  
  <pre><code>./stringtie G1_sorted.bam -B -o G1.gtf -G Triticum_aestivum.IWGSC.42.gtf -p 4  -C G1.refs.gtf -A G1.abund.tab
  </code></pre>
  
  <p>Error is:</p>
  
  <pre><code>-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.
  </code></pre>
  
  <p>How can I resolve it?</p>
  
  <p><strong>Update:</strong></p>
  
  <p>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:</p>
  
  <pre><code> &gt;1A dna:chromosome chromosome:IWGSC:1A:1:594102056:1 REF
  CTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCCTAACCCTAAACCCTAACCAAAAC
  </code></pre>
  
  <p>Where as The annotation file (gtf file ) is as                                                                                                 </p>
  
  <pre><code>    #!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"; 
  </code></pre>
  
  <p>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 ?</p>
   1135: <p>This seems to be a common problem. As @llrs pointed out, Ensembl, UCSC(genome browser and associated data) and NCBI records are not directly interchangeable. The ambiguity refers to annotation as well as the reference genome. The reference genome is identical, except for the chromosome naming convention, meaning a reference from Ensembl might not contain CHR prefix, whereas it will be present in one downloaded from UCSC.</p>
  
  <p>To prevent such conflicts in downstream tools, it is good to stick to the reference and annotation from the same repository throughout the analysis and map the genes to gene names or whatever towards the end of the investigation. </p>
  
  <p>You can download all the associated data for <em>T. aestivum</em> which I beleive is the organism you want to study from Ensembl plants FTP <a href="http://plants.ensembl.org/info/website/ftp/index.html" rel="nofollow noreferrer">download</a>. </p>
  