# Assembly by stringtie

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 ?

• This looks like your chromosome names in the BAM don't match the GTFs you're using. Check that first. Mar 6 '19 at 18:53
• the reference genome download from the NCBI.and gtf file from ensembl. your mean is that i have to use the gtf file from the NCBI, then this error will be removed? Mar 7 '19 at 4:17
• Welcome to the site @fatima. Yes ENSEMBL uses genes identifiers starting with ENSGXXXXX.XX while NCBI uses gene names with just numbers and they don't map to the same positions. They aren't exacts equivalent
– llrs
Mar 7 '19 at 8:35
• hi IIrs, i have use the reference genome and gtf file from ensembl.encounter same problem.how i can mofify the file with same name? Mar 9 '19 at 18:34
• hi @fatima (to send me a notification use @ followed by my username) Could you please explain how do you want to modify these files to use the same name? rereading again your question I find it a bit unclear what do you want to achieve and what do you expect us to do for you.
– llrs
Mar 12 '19 at 14:04