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: interval consistency in diagnostic alignment tables #319
Alignment tables are produced for each library when the --diagnostics / -d option is passed to tiny-count, and these tables contain helpful information about each alignment including positional information, the sequence’s raw/normalized read count, the number of overlapping candidate features, and any features that were selected for read assignment.
Features and alignments are represented internally with a 0-based interval, and this interval’s coordinates are provided in the alignment tables. However, since the GFF and SAM specifications use a 1-based interval, alignment tables will be updated to use the same convention.
Alignment tables are produced for each library when the
--diagnostics/-doption is passed to tiny-count, and these tables contain helpful information about each alignment including positional information, the sequence’s raw/normalized read count, the number of overlapping candidate features, and any features that were selected for read assignment.Features and alignments are represented internally with a 0-based interval, and this interval’s coordinates are provided in the alignment tables. However, since the GFF and SAM specifications use a 1-based interval, alignment tables will be updated to use the same convention.