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Hello,
I ran RaGOO v1.1 with default parameters: python ragoo.py contigs.fasta ref.fasta -t10
I looked for two specific contigs in the results which I know should map one after the other to chromosome 4. I looked at the paf output:
However, when looking at orderings/4_orderings.txt , only the first contig is there, while the second went to Chr0. Same when I look at groupings/4_contigs.txt.
Can you help me understand why the second contig was added to Chr0? it looks like it maps pretty well to the reference.
Thanks!
The text was updated successfully, but these errors were encountered:
My guess is that the alignment was too small (< 1 kbp) to be considered. Unfortunately, this is not a tunable parameter (though it will be in v2).
If using default settings, you can manually changes this by editing line 590 in ragoo.py. Just change l to be a smaller number - perhaps 600 in your case.
Hello,
I ran RaGOO v1.1 with default parameters:
python ragoo.py contigs.fasta ref.fasta -t10
I looked for two specific contigs in the results which I know should map one after the other to chromosome 4. I looked at the paf output:
However, when looking at orderings/4_orderings.txt , only the first contig is there, while the second went to Chr0. Same when I look at groupings/4_contigs.txt.
Can you help me understand why the second contig was added to Chr0? it looks like it maps pretty well to the reference.
Thanks!
The text was updated successfully, but these errors were encountered: