Comments (1)
Ideally, in the two fasta files, sequences corresponding to the same chromosomes should have exactly same identifiers. For example:
##File1.fa
Chr1
ATGCGGAT
Chr2
GTCAAGTC
##File2.fa
Chr1
GACTATGC
Chr2
GGTCAGGT
When there is a discrepancy in the identifiers, SyRI tries to match chromosomes in the two fasta files using their alignment information. However, sometimes it is not possible to automatically match chromosomes (like in the above case). This issue can be resolved by manually fixing the chromosome identifiers, so that corresponding chromosomes in the two fasta files have exactly the same identifiers.
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Related Issues (20)
- Inversion disappears after running chroder HOT 3
- high fraction of inverted alignments HOT 2
- Installation error with conda create HOT 8
- KeyError thrown when running example with v1.6.3 HOT 6
- 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
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