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: new selector for filtering alignments by edit distance #296
In the SAM specification, NM:i: tags indicate an alignment's edit distance to the reference (if mismatches are allowed). A new selector, Mismatches, will be added to the Features Sheet so that selection rules can be defined to filter reads by this value in Stage 3. It will support single values, lists, or ranges just like the Length selector.
The NM:i: tag is optional, and while it is reported by bowtie it isn't reported by all alignment tools. If it is missing then the edit distance will have to be calculated by parsing the CIGAR string.
In the SAM specification,
NM:i:tags indicate an alignment's edit distance to the reference (if mismatches are allowed). A new selector,Mismatches, will be added to the Features Sheet so that selection rules can be defined to filter reads by this value in Stage 3. It will support single values, lists, or ranges just like theLengthselector.The
NM:i:tag is optional, and while it is reported by bowtie it isn't reported by all alignment tools. If it is missing then the edit distance will have to be calculated by parsing theCIGARstring.