Mapping a draft sequence to a finished sequence using MUMmer.
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?
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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.