I quantified some samples using Salmon. According to the documentation of output format, the last column of the 'Quantification File' represents the number of reads that supported the given transcript, namely:
NumReads — This is salmon’s estimate of the number of reads mapping to each transcript that was quantified. It is an “estimate” insofar as it is the expected number of reads that have originated from each transcript given the structure of the uniquely mapping and multi-mapping reads and the relative abundance estimates for each transcript.
In some case, I had in the output some transcripts that had
NumReads=0.000000. Does this mean that I should discard them from the list of transcripts obtained in that sample? How comes that those transcripts end up in the output file in first place, since they don't have any reads support and the quantification was done using the reads themselves?