Question: STRINGTIE WARNING: no reference transcripts were found for the genomic sequences where reads were mapped
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gravatar for hirahameed222
6 months ago by
hirahameed2220 wrote:

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.

rna-seq assembly • 369 views
ADD COMMENTlink written 6 months ago by hirahameed2220

It is an issue with the GTF file downloaded from NCBI. Check this post

Warning encountered while transcript abundance estimation using stringtie

ADD REPLYlink written 6 months ago by lakhujanivijay4.4k

Can you please suggest the suitable Reference genome for wheat and Gtf/gff3 file for wheat to avoid such error . I would be very thankful if you can help me in providing these (links) since i tried and tested many RefGenomes (even few top level too) but everytime i got the same error.

ADD REPLYlink written 6 months ago by hirahameed2220
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