Salmon output: transcripts quantified with zero reads support
All transcripts should always be returned in the output, whether there's evidence supporting their expression or not. This is for the sake of simple convenience, since typically one would be merging these values across samples into a matrix. Missing values will then tend to become either NA or cause an error, when what would be appropriate would be to have values of 0. This also facilitates calculations such as "what's the median number of reads per transcript?" or "what percent of transcripts have an expected reads count of at least X".