Mapping a draft sequence to a finished sequence using MUMmer.
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12 months ago

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?

MUMmer • 310 views
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What exactly is not working? It seems MUMmer have performed the alignment just fine.

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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.

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0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

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