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: additional fields in diagnostic alignment tables #308
tiny-count produces alignment tables for each library when diagnostics are requested (--report-diags).
Each row in the alignment table describes a read alignment and the features it was assigned.
The following columns will be added to alignment table outputs:
Column
Description
Raw count
The sequence's original, non-normalized count
Genomic hits
The number of alignments reported for the sequence
Feature Aliases
The user-defined aliases for the assigned features, if any
Mismatches
The number of mismatches between the query sequence and the reference
The following additional changes will be made to the column reporting features assigned to the alignment:
Rename Assigned Features -> Feature Hits, for consistency
Produce a more easily parseable string format, e.g. (feat_id_1, classifier); (feat_id_2, ); ...
Produce empty cells for alignments without feature hits rather than NONE
tiny-count produces alignment tables for each library when diagnostics are requested (
--report-diags). Each row in the alignment table describes a read alignment and the features it was assigned.The following additional changes will be made to the column reporting features assigned to the alignment:
(feat_id_1, classifier); (feat_id_2, ); ...NONE