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  • HTSeq-count returns all 0's?

    I am using HTSeq-count to count the number of gene features in my RNA-seq samples. I did the original alignment using HISAT2 with a FASTA file, and the HTSeq-count with a GTF file from the same website (Gencode). The command I used is shown below.

    htseq-count -f bam sample.sorted.bam GRCh38_genome.gtf > sample_htseqcount.txt

    The output is a file containing all 0's for the counted features. I have read on forums this may be due to the gene names being different in the FASTA and GTF files used for the alignment and counting. Does anyone know how to fix this problem? How do I change the gene names to match in both files?

    Thanks in a advance!

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