Cannot find a gene in the counts table

Question

[felipead66]

I have human rna-seq data and I use the tophat/samtools/htseq pipeline to produce the count table. My problem is that a particular gene, does not appear in the final count table, although it appears on the .gtf file. What could be the reason for that? Shouldn't all genes in the .gtf file appear in the count table?

[piyushjo]

Is that only that gene or there are others like that? Did you do any filtering? Does the gene have exons in the GTF? What is the name of that gene? Little more details would be helpful!

[ATpoint]

Please add code.