Comments (2)
Hi,
The first warning message:
Reference chromosome CP007726.1 do not have any directed alignments with its homologous chromosome in the query genome (tig00000001). Filtering out all corresponding alignments.
Suggests that the homologous chromosomes might have different strands (check #48). Reversing complementing the chromosomes to ensure that same strands are being compared should fix this issue.
The second error message is most probably also caused because of this.
You can try fixchr to get consist strands for chromosomes.
from syri.
Thank you, that was it!
from syri.
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