I am trying to calculate the depth coverage between short read and long read in rna-seq. Below screenshot is the output file, [prefix]_Log.final.out.
My understanding of calculating the coverage in short read is read_length #_aligned_reads which gives 88 36385382. But, when we say coverage, it's represented as 40 x (every base in the static length genome is covered 40 times with reads).
Any help would be appreciated how to get the coverage like x10 in short read and long read. First, how do you calculate coverage in short read based on the screenshot below?
You will want to use a program that will calculate this instead of using this log file. One example
It may also be worth considering this: What exactly is sequencing depth in RNAseq?