Here is the situation: I want to count the reads number of spike-in sequences of an RNA-seq project. And I already mapped the reads to both the human genome and spike-in sequences, and got the bam files. Then I tried to use featurecounts tool to quantify the reads number of both genes and spike-in sequence, so I make up the spike-in GTF file and add them to the GRch38 version gtf file. The file looks like this:
I thought I 've made this correctly, but the output file of featurecounts never contained the "GLuc" or "CLuc" gene. Here are the head lines of the output:
I really don't know how to solve this. Is there anyone can help me out. Thanks a lot.