Comments (3)
HDRs are defined in figure S8 in the supplementary material. Basically, they are regions with gaps in both genomes in-between two alignments of an annotation-block.
from syri.
Thanks, so they are regions that encompass {SYN - NOTAL - SYN} arrangements.
from syri.
Not really.
SyRI first performs structural annotation of the genomes. Regions which are not aligned and are not part of any annotation block are called NOTAL. Within each annotation block, syri checks the overlaps and gaps between consecutive alignments (if any), and annotates sequence variations like CNVs, HDRs etc. The distinction between a NOTAL and HDR is that the HDRs have associated structural annotation (for example: a HDR within an overall syntenic/translocated region), whereas no structural annotation is possible for the NOTAL regions as they are unique to the genomes.
from syri.
Related Issues (20)
- Import Error HOT 1
- the parameter --reg can not show Translocation HOT 1
- The question with "Unequal number of chromosomes in the genomes" error HOT 1
- Issue of choice of aligner for whole genome alignment of two set of genomes HOT 2
- SAM reader - ERROR - Incorrect CIGAR string found. CIGAR string can only have I/D/H/S/X/=. CIGAR STRING: CM028859.1 HOT 2
- Cython package not detected HOT 3
- Erro in reading BAM file. reference_id -1 out of range HOT 1
- Synteny differs between same set of assemblies HOT 5
- Genome specific sequences HOT 3
- Chromosomes IDs do not match HOT 2
- IndexError: list index out of range (but no error when swapping the reference and query) HOT 7
- generating table output error HOT 2
- Error when using .SAM file HOT 18
- Incorrect CIGAR string found. HOT 6
- unequal chromosomes HOT 3
- empty output of chroder HOT 6
- AttributeError with syri HOT 1
- IndexError: list index out of range HOT 5
- missing parameter HOT 1
- REF and ALT start positions do not match HOT 1
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from syri.