Next – Generation Sequencing

Once download is complete, unzip the archive and copy featureCounts executable file from “bin”
folder and paste it in our working directory. Type the following command to get gene level
summarized read counts.

featureCounts -p -T 4 -M -O -a human_grch37.gtf -o gene. expression.txt
normal.sorted.bamtumor.sorted.bam

-p for paired end reads
-T number of processors to use
-M to consider multimapped reads
-O to consider overlapping reads
-a genome annotation file
-o output filename

The output file gene.expression.txt is a tab delimited text file which can be opened with a
spreadsheet application. Transcript level expression can be calculated by providing an extra option –
-g “transcript_id”.