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Stringtie error with gtf file

Hi! I am getting this error when I try to run stringtie on some RNA-seq data. This is what I am getting. 

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.

I am using a gtf file from flybase. I am wondering if it is just not the correct file? I am working on a project with Drosophila. Does anyone know anything about this or could help?

The index that I used for hisat2 was just the premade Drosophilia index they have on their site. Could it be an issue of the index is a older version than the gtf file?

Thanks in advance

rna-seq software error next-gen
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written by williamsbrian5064 williamsbrian5064

It seems that the header of reference fasta file and naming used in gtf/gff (1st column ) is not matching. Have you downloaded reference fasta & gtf/gff file from same DB and is it of similar version?

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written by MSM55 MSM55

I believe a similar version. Do you think that is the issue?

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written by williamsbrian5064 williamsbrian5064

Where did you get the indexes from? Can you post the output of following commands (use real file names that you have)

$ grep "^>" genome.fa 
$ head -10 your_file.gtf
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written by GenoMax GenoMax

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