I am doing paired end RNA-seq analysis. I used STAR mapper and then StringTie for getting quantification of my data. After successfully running StringTie, I got
.gtf files which will give me information about genes, their coverage along with TPM and FPKM values. It also produced some more
I want to know how what percentage of my reads mapped to reference genome. I know this can be done with BAM or BED files produced after STAR alignment. However, I want to know if this can be done with output files generated by StringTie?
I just want to clarify my question after reading comments and answers I am getting. I want to know if this can be done with
.gtf files of StringTie. As I mentioned before, I already know how to achieve this with BAM files. This is little bit weird situation because, I have deleted my BAM files to get more space on my hard drive. So I could just run entire analysis again, but wanted to know if it is possible without redoing whole analysis. Apologies for the confusion.