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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tiny-count: consistency and auto-documentation changes in outputs #310
The QNAME field in decollapsed outputs currently retains the count= of the original alignment. This means that reads would be over counted if a user ran these decollapsed outputs back through tiny-count (thus squaring total mapped reads). This is certainly an uncommon use case, and inadvisable since it would increase runtimes with no added benefit, but we want to ensure it is possible nonetheless.
Prefixed Features Sheet Output During Standalone Runs
The tinyRNA pipeline currently provides a copy of the Features Sheet in tiny-count's output subdirectory for auto documentation. Standalone runs do not, so tiny-count will be updated to so. The copy's filename will be prefixed to match the other outputs.
Decollapsed Outputs
The QNAME field in decollapsed outputs currently retains the
count=of the original alignment. This means that reads would be over counted if a user ran these decollapsed outputs back through tiny-count (thus squaring total mapped reads). This is certainly an uncommon use case, and inadvisable since it would increase runtimes with no added benefit, but we want to ensure it is possible nonetheless.Prefixed Features Sheet Output During Standalone Runs
The tinyRNA pipeline currently provides a copy of the Features Sheet in tiny-count's output subdirectory for auto documentation. Standalone runs do not, so tiny-count will be updated to so. The copy's filename will be prefixed to match the other outputs.