tinyRNA provides an all-in-one solution for precision analysis of sRNA-seq data. At the core of tinyRNA is a highly flexible counting utility, tiny-count, that allows for hierarchical assignment of reads to features based on positional information, extent of feature overlap, 5’ nucleotide, length, and strandedness.
Case sensitivity is no longer required in the Select for... and with value... columns. More specifically, case does not need to match when examining a feature's attributes for an identity match. The original capitalization of both the attribute key and value is retained after a match is found, so capitalization in Counter's outputs will not be affected by this change.
The Class attribute is no longer required to be present in each feature's column 9 attributes. If the attribute is missing, a default Class value of _UNKNOWN_ will be assigned to the feature. This default assignment takes place before stage 1 selection, so users may also define rules that Select for: Class, with value: _unknown_
The GFF2 / GTF is now listed as a supported format in the documentation, and references to GFF3 have been replaced with GFF to indicate wider support. This didn't require any code changes since the two formats are similar enough to GFF3 and HTSeq's GFF parser automatically handles the minor differences between formats.
Case sensitivity is no longer required in the
Select for...andwith value...columns. More specifically, case does not need to match when examining a feature's attributes for an identity match. The original capitalization of both the attribute key and value is retained after a match is found, so capitalization in Counter's outputs will not be affected by this change.The Class attribute is no longer required to be present in each feature's column 9 attributes. If the attribute is missing, a default Class value of
_UNKNOWN_will be assigned to the feature. This default assignment takes place before stage 1 selection, so users may also define rules thatSelect for: Class, with value: _unknown_The GFF2 / GTF is now listed as a supported format in the documentation, and references to GFF3 have been replaced with GFF to indicate wider support. This didn't require any code changes since the two formats are similar enough to GFF3 and HTSeq's GFF parser automatically handles the minor differences between formats.
Closes #181