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banzhou59 / GenomeSyn

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Collinear areas are not displayed #3

Open ji-yu1 opened 6 months ago

ji-yu1 commented 6 months ago

I used "GenomeSyn -g1 24.Chr2A.fasta -g2 19_Chr2A.fasta -cf1 19-24.filter.coords" without any errors, but there were no collinear segments in the drawing results. Can you help me take a look at this issue? The coords file is as follows: 屏幕截图 2024-05-12 190038

banzhou59 commented 6 months ago

Can you see the parameters for running Mummer? My coords file has 13 columns, please run the following commands: nucmer -t $use_threads -g 1000 -c 90 -l 40 -p $index_name $ref_file $query_file delta-filter -r -q -l 1000 $index_name.delta >$index_name.delta.filter show-coords -TrHcl $index_name.delta.filter >$index_name.delta.filter.coords I hope the above answers can help you. 1

ji-yu1 commented 6 months ago

Thank you very much for your help! I used the parameters you provided to run and obtained the correct file and image!