Good day,
Help me please with plotting mummer alignment.
I've created out.mums file with command
../sparseMEM/mummer -mum -b reference.fa query.fa >out.mums.
Both input fasta file are multi-fasta sequences, ~9.000 of records in each. Actually it is a draft assemblies.
When I am trying to plot it using mummerplot,following the documentation, I always receive an error:
" set ticscale 0 0
^
"mummer.gp", line 13: warning: Deprecated syntax - please use 'set tics scale' keyword
"
Then I've tried to create small test *.mums file with usual mummer command
../mummer-3.22/mummer -mum -b -c testReference.fa testQuery.fa >testOut.mums
But mummerplot could not plot *.mums file, it returns the same error.
When I used nucmer for aligning, it has created *.delta file, and this delta file is plotting perfectly. But for my real files usual mummer and nucmer always crashes with segmentation fault error.
I need to create dot-plot, so what you'll suggest me to do?
Regards,
Vlasova Anna
---------------------------------------------
Bioinformatica i Genomica
CRG-Centre for Genomic Regulation
C/ Dr. Aiguader, 88
Edif. PRBB
08003 Barcelona, Spain
Help me please with plotting mummer alignment.
I've created out.mums file with command
../sparseMEM/mummer -mum -b reference.fa query.fa >out.mums.
Both input fasta file are multi-fasta sequences, ~9.000 of records in each. Actually it is a draft assemblies.
When I am trying to plot it using mummerplot,following the documentation, I always receive an error:
" set ticscale 0 0
^
"mummer.gp", line 13: warning: Deprecated syntax - please use 'set tics scale' keyword
"
Then I've tried to create small test *.mums file with usual mummer command
../mummer-3.22/mummer -mum -b -c testReference.fa testQuery.fa >testOut.mums
But mummerplot could not plot *.mums file, it returns the same error.
When I used nucmer for aligning, it has created *.delta file, and this delta file is plotting perfectly. But for my real files usual mummer and nucmer always crashes with segmentation fault error.
I need to create dot-plot, so what you'll suggest me to do?
Regards,
Vlasova Anna
---------------------------------------------
Bioinformatica i Genomica
CRG-Centre for Genomic Regulation
C/ Dr. Aiguader, 88
Edif. PRBB
08003 Barcelona, Spain
Comment