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MontgomeryLab / tinyRNA

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.
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Counter, DGE, Plotter: optionally multi-indexed feature counting using tagged rules #200

Closed AlexTate closed 2 years ago

AlexTate commented 2 years ago

Tagged feature counting is now supported.

Counts assigned by tagged rules are specifically counted as a feature and tag pair, or match ID, and feature_counts.csv is now indexed by this match ID rather than feature IDs alone. Features which match a tagged rule retain the same metadata (class, alias, discontinuous feature relationships) but are otherwise counted as distinct features when they are selected by one of these rules. These count subsets are pooled between rules when multiple rules define the same tag. This behavior extends to DGE analysis, and class counts from tagged rules receive the corresponding label in class_charts and sample_avg_scatter_by_dge_class.

Closes #197

taimontgomery commented 2 years ago

Looks great! In the next update, we need to change the name of one of the _norm_counts.csv files because the file in counter is assigned the same name as the file in DGE. Maybe change _norm_counts.csv in DGE to _DESeq2_counts.csv.