I have RNA-seq data and I aligned it with tophat to human genome reference from UCSC. I also download the human gene transcript file from UCSC. After I do the alignment with tophat, I tried to follow this method: http://www.bioconductor.org/help/workflows/rnaseqGene/
I already get the count reads matrix from my data after I perform summarizeAlignment. The problem is, I need to check for several specific gene (I checked the gene id from UCSC gene browser) and I get all 0 value from the count reads matrix for my specific genes. I believe if the count reads is 0 there is nothing to analyze but I think it is impossible because I know that for that gene, it will be expressed quite a lot from that tissue. I think I made a mistake in my procedure even though I followed exactly as the example. Can you all give some suggestion at what point probably I made a mistake? My code is exactly the same as the example. Thank you.