BioC 3.8 was just released and there is a great new package tximeta (at least if you work with Salmon). I am still trying to properly understand how it works. The vignette contains the following section:
However, to avoid downloading remote GTF files during this vignette, we will point to a GTF file saved locally (in the tximportData package). We link the transcriptome of the Salmon index to its locally saved GTF. The standard recommended usage of
tximeta would be the code chunk above, or to specify a remote GTF source, not a local one. This following code is therefore not recommended for a typically workflow, but is particular to the vignette code.
Why is it not recommended to point to the locally saved GTF? I assume this is to allow for more reproducible analysis, but the primary input for the tool are Salmon files that were already run with a locally saved index and the same index is passed to
makeLinkedTxome() as well. If certain reference files are already local anyway, why not just keep them all local?