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.
The recent integration of pysam has created an opportunity for supporting the BAM format for alignments.
[x] Modify load_samples() to allow alignment files that have a .bam extension
[x] Rename SAM_reader to AlignmentReader
[x] Update AlignmentReader class to require BAM file @HD headers to report either SO:queryname or GO:query so that normalization by genomic hits can be performed properly
The recent integration of pysam has created an opportunity for supporting the BAM format for alignments.
@HDheaders to report eitherSO:querynameorGO:queryso that normalization by genomic hits can be performed properly