In the Stringtie2 paper, it is briefly mentioned that --mix mode uses short reads for the splice junction correction. So, I as wondering in the output gtf file generated using --mix mode, what does the coverage in the last column incorporate? Does it incorporate both long and short reads. Also, how is cov calculated or how is it exactly defined in stringtie? When I run stringtie with -e and -L options I should expect the coverage to be lesser than --mix (both long and short bam files) mode, but the output turned out to be opposite for at least one transcript of my interest. Can you shed some light on this issue?
Hello,
In the Stringtie2 paper, it is briefly mentioned that --mix mode uses short reads for the splice junction correction. So, I as wondering in the output gtf file generated using --mix mode, what does the coverage in the last column incorporate? Does it incorporate both long and short reads. Also, how is cov calculated or how is it exactly defined in stringtie? When I run stringtie with -e and -L options I should expect the coverage to be lesser than --mix (both long and short bam files) mode, but the output turned out to be opposite for at least one transcript of my interest. Can you shed some light on this issue?
Thanks Ayush