Closed AlexTate closed 1 year ago
Reopening this issue to add support for the Classify as...
values in this mode. They're illustrated as being part of Stage 1 selection so I didn't include them in order to avoid confusion and be consistent with "Stage 1 selection is skipped." With the current explanation of "these reference sequences behave like features that had matched every rule in Stage 1," I think we could include them without adding too much confusion.
The pipeline currently requires the user to specify at least one reference GFF. However, there may be instances where they don't have or want to use genomic/reference annotations (.fa/.gff). For example, instead of a genomic fasta file they may instead want to use a synthetic fasta with known sequences to count against.
The behavior of tiny-count will be changed to allow for this. If a user does not specify any GFF files:
@SQ
flags in input SAM files.