With bowtie2-build I have created an index file of the arabidopsis Araport11 genome (https://www.arabidopsis.org/download/index-auto.jsp?dir=%2Fdownload_files%2FGenes%2FAraport11_genome_release) where I have used Araport11_cdna_20160703_representative_gene_model.gz for a transcriptome. Then I have created .bam files of my single-end reads with bowtie2, and converted them to .bam with samtools sort. What I'ld like to do now is create a read count csv file, as well as gtf file with stringtie. For this I got these files for annotation guides: Araport11_GFF3_genes_transposons.201606.gff.gz & Araport11_GFF3_genes_transposons.201606.gtf.gz. I applied gunzip on these files.
However, when I try to run stringtie {input} -eB -G {either of the .gff or .gtf guides} -o {output}
I get the following warning for both the .gff- and .gtf guide files: 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.
And when then running prepDE.py, it contains appropriate arabidopsis AGIs as rows, and appropriate sample-specific columns (representing reads of each sample). ALL values in the file are zero, however!
Clearly something must have gone wrong. Also when manually searching for genes that are listed in my .bam files in the .gff and.gtf files, there are in fact results! So it does seem that the same naming convention is correct. What am I doing wrong here?