no reference transcripts were found for the genomic sequences where reads were mapped!

[TommySchooner]

Hi there,

I am trying to use a reference guided annotation assembly for Stringtie. The gtf file is self made, and the bam files contain the fastq files.

I use the command:

stringtie -L -G /Users/apple/Desktop/Final_Project/0_Reference_genomes/HB9_annotation_White/RNAseq-HB9.gtf -o HB9_stringtie2_full.gtf /Users/apple/Desktop/Final_Project/1_Mapping_human_genome/WTw_minimap2_HPC_minimap2/WTw_HB9_sorted.bam

However, it shows the following error:

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 wonder how to solve the issue, since I am using a self-made gtf file? Thank you!

Best regards

[NoMatter-98]

Hi there, I met the same problem, and did you deal with it ?

[ngsguru]

I solved this issue by simply deleting every "chr" which shows chromosome number in the gtf file: mm10.ncbiRefSeq.gtf (saved as mm10.ncbiRefSeq_MODIFIED.gtf) . i.e., replaced "chr1 to chr22" with "1 to 22" stringtie -p 8 -G GTF_FILES/mm10.ncbiRefSeq_MODIFIED.gtf -o STRINGTIE/Trim_MT1_chr19.gtf -l MT1 SAMTOOLS/Trim_MT1_chr19.bam

[xue-222]

我通过简单地删除gtf文件中显示染色体编号的每个“chr”来解决此问题：mm10.ncbiRefSeq.gtf（另存为mm10.ncbiRefSeq_MODIFIED.gtf）。即，将“chr1 to chr22”替换为“1 to 22” stringtie -p 8 -G GTF_FILES/mm10.ncbiRefSeq_MODIFIED.gtf -o STRINGTIE/Trim_MT1_chr19.gtf -l MT1 SAMTOOLS/Trim_MT1_chr19.bam

why did you do it?

[xue-222]

I tried and still couldn't solve the problem

[Endeavor326]

I also meet this problem, I will try this way.wait me