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3.5 years ago
sharmatina189059
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110
Can anybody tell me why MUMmer is not working?
nucmer --prefix=ref_qry ref.fasta qry.fasta
show-coords -rcl ref_qry.delta > ref_qry.coords
show-aligns ref_qry.delta refname qryname > ref_qry.aligns
I am confused with refname and qryname. What are those ids. The coordinate file shows:
[S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] | [LEN R] [LEN Q] | [COV R] [COV Q] | [TAGS]
===============================================================================================================================
1 14175 | 205133 219307 | 14175 14175 | 97.91 | 4004792 636544 | 0.35 2.23 | gi|1122346792|ref|NZ_CP018664.1| NODE_1_length_636544_cov_49.323596
14193 45396 | 242485 273682 | 31204 31198 | 98.94 | 4004792 636544 | 0.78 4.90 | gi|1122346792|ref|NZ_CP018664.1| NODE_1_length_636544_cov_49.323596
45796 46499 | 274447 275150 | 704 704 | 99.43 | 4004792 636544 | 0.02 0.11 | gi|1122346792|ref|NZ_CP018664.1| NODE_1_length_636544_cov_49.323596
What id I can give to this command? also, How to plot that using mummer plot?
What exactly is not working? It seems MUMmer have performed the alignment just fine.
What should be given in the step given below:
show-aligns ref_qry.delta refname qryname > ref_qry.aligns
What is refname and qryname and how to plot this alignment.
show-aligns ref_qry.delta refname qryname > ref_qry.aligns
I could not understand What is refname and qryname and how to plot this alignment. Please help.
What should be given in the step given below:
show-aligns ref_qry.delta refname qryname > ref_qry.aligns
What is refname and qryname and how to plot this alignment.