sorted bam file generated from gff transcript fastas, how to get counts with HTseq?

Question

[RNAseqer]

I have a single cell miRNA analysis. I have generated a sorted bam file using STAR with the mirbase hairpin fastas and the hsa.gff3. I generated a genome index with star then performed alignment. Now however, I want to get the counts for my miRNAS, and HTseq complains:

*
    Warning: No features of type '{args.feature_type}' found. 
    The alignment file has no chromosomes in common with the GFF/GTF file. This will 
    result in zero feature counts. Please check if the references match, 
    e.g. if you are using 'chr1' or '1' as chromosome names.
*

So, since the hairpin fasta had no chromosome number in its identifier and my bam lacks this info, how do I approach this?

[Pierre Lindenbaum]

Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.

• junction_annotation.py: How many 'novel' splice junctions/splice events are resonably expected from human RNA,
• coef /makeContrasts very different results
• mirge3.0 custom miRNA db option
• WGCNA: outputting multiple hubgenes from a module
• How to extract beta coefficients from edgeR output
• EdgeR exclude 0 count subjects for each gene
• Analysis of a SNPs moderating effect on disease
• chi squared assesment of gene expression and batch effect
• model matrix error message 'unequal columns/rows' when using a conditional variable
• GSEA pvalue output of 0.0. Can I make it more specific?
• Is there a good reference matrix for miRNA array deconvolution?
• Small number of genes, drop in sft fit curve at higher threshold powers. why?
• how to adjust for continuous covariates in limma?
• batchCombat package for R?
• limma, best practices review paper?
• minimum snp number from set in LD
• Default Plink Window size?
• Plink recode option to get genomic position?
• samtools sam-to-bam conversion => bamfile RSeQC tool bam_stats.py cannot use. ValueError: file has no sequences defined (mode='rb')