May want to use the 'ts' or 'TS' or 'XS' tag for strand rather than raw read strand
'ts' is a minimap2 specific tag (not standardized, but common, used in screenshot below)
'TS' is standardized
'XS' is a vintage tag seen in older aligners, data exists for it
Raw read strand is a mix of + and - but the ts tag can indicate the actual strand to use
The jbrowse sashimi arcs are colored using this
Example with creating a from negative strand read, but it is a positive strand gene
(minimap2 "transcript strand" https://lh3.github.io/minimap2/minimap2.html)
TS:A:strand Strand (‘+’ or ‘-’) of the transcript to which the read has been mapped https://samtools.github.io/hts-specs/SAMtags.pdf
May want to use the 'ts' or 'TS' or 'XS' tag for strand rather than raw read strand
'ts' is a minimap2 specific tag (not standardized, but common, used in screenshot below)
'TS' is standardized
'XS' is a vintage tag seen in older aligners, data exists for it
Raw read strand is a mix of + and - but the ts tag can indicate the actual strand to use
The jbrowse sashimi arcs are colored using this
Example with creating a from negative strand read, but it is a positive strand gene
(minimap2 "transcript strand" https://lh3.github.io/minimap2/minimap2.html)
TS:A:strand Strand (‘+’ or ‘-’) of the transcript to which the read has been mapped https://samtools.github.io/hts-specs/SAMtags.pdf