How to extract genes from RNA-seq using its reference genome?

Question

[ivan.nikolaev025]

Hi, I am fairly new to Bioinformatics. I have been working on a way to extract genes from RNA-seq using its reference genome, E.coli K-12. I have managed to align the two using HISAT-2 but now I am stuck. How do I go about getting a list of genes from the RNA-seq data?

[GenoMax]

How do I go about getting a list of genes from the RNA-seq data?

E. coli has a well characterized genome so we know where all the genes are. Are you referring to getting read counts for those known genes? If so you do that by using your aligned/sorted BAM files and programs such as featureCounts (part of subread package) or htseq-count.