mummer-help Mailing List for MUMmer (Page 2)

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Hello,

Can anyone please tell me the meaning of M-to-M alignments mean ? I
understood that 1-to-1 means number of unique alignments.

Thanks,
AP

Hi Katharine,
Repeats can be tricky to align properly. For the most conservative
approach, I would recommend aligning with -maxmatch, and then running
show-snps with the -C option enabled, which will suppress SNPs contained
w/in any repeats. Running nucmer with -maxmatch will ensure that the
show-snps program 'sees' all the repeat alignments, so that you can exclude
them and focus only on the uniquely aligned regions.

Best,
-Adam

On Mon, Sep 24, 2018 at 3:30 PM Katharine Walter <kw...@st...>
wrote:

> Hi all,
>
> I am using MUMMER to identify SNPs between two bacterial genomes. I'm
> hoping to identify SNPs in regions of 1-1 mapping between the genomes, that
> do not fall within repetitive regions. I'm a bit confused about two items:
> 1) nucmer -maxmatch vs -mum:
> When I use nucmer -maxmatch, I identify 1132 SNPs. This number increases
> to 1315 with -mum. I did not expect this, because I thought the anchors
> would be constrained to unique regions with -mum.
> 2) the use of delta-filter.
> When I use delta-filter -1 (or -r -q) to filter out repetitive regions, I
> identify more SNPs. Again, I expected to remove SNPs with this filter.
>
> Any suggestions would be great.
> Thank you!
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>

Hi all,

I am using MUMMER to identify SNPs between two bacterial genomes. I'm
hoping to identify SNPs in regions of 1-1 mapping between the genomes, that
do not fall within repetitive regions. I'm a bit confused about two items:
1) nucmer -maxmatch vs -mum:
When I use nucmer -maxmatch, I identify 1132 SNPs. This number increases to
1315 with -mum. I did not expect this, because I thought the anchors would
be constrained to unique regions with -mum.
2) the use of delta-filter.
When I use delta-filter -1 (or -r -q) to filter out repetitive regions, I
identify more SNPs. Again, I expected to remove SNPs with this filter.

Any suggestions would be great.
Thank you!

Great, thanks!

On Fri, Sep 21, 2018 at 10:41 AM Adam Phillippy <aph...@gm...>
wrote:

> Correct! Everything is 1-based.
>
> On Fri, Sep 21, 2018 at 1:31 PM Katharine Walter <kw...@st...>
> wrote:
>
>> Hi,
>> I just wanted to confirm - mummer outputs (snp positions) are 1-based,
>> correct? Thank you!
>> _______________________________________________
>> MUMmer-help mailing list
>> MUM...@li...
>> https://lists.sourceforge.net/lists/listinfo/mummer-help
>>
>

Correct! Everything is 1-based.

On Fri, Sep 21, 2018 at 1:31 PM Katharine Walter <kw...@st...>
wrote:

> Hi,
> I just wanted to confirm - mummer outputs (snp positions) are 1-based,
> correct? Thank you!
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>

Hi,
I just wanted to confirm - mummer outputs (snp positions) are 1-based,
correct? Thank you!

Dear all,

We are observing unexpected results in the comparison of 3 genomes, and I wonder if you could provide any insights on how this is possible, and if it could be a bug, or an error on our end.
We have two reference genomes that are fairly similar (picture attached - C4 vs C5). We compare our draft assembly to each one of them and get drastically different results.
How can the two references appear so similar to each other (C4 X C5) and my draft assembly be so different to one (C5 x R3) but so similar to the other (C4 X R3)?

Nucmer (version 3.23) /mummer was run for each comparison with the following codes:
nucmer -maxmatch -c 100 -p nucmerC4XC5 C4.fasta C5.fasta
show-coords -r -c -l nucmerC4XC5.delta > nucmerC4XC5.coords
mummerplot -f -p nucmerC4XC5 -l --large --png nucmerC4XC5.delta

Thank you very much,
Marcio Resende

[cid:9AF...@uf...]

Hi,
I was tying out the nucmer function of Mummer, but  have problem plotting
it. I wanted to plot an identity plot, like the one plotted in Fig 3 of
this paper -
https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-291#Fig3
I tried using the mummerplot function, but the resulting plots are not like
the one in the paper. Additionally I have some errors too.

If you can kindly help, I will let you know the details.

Thank you
Regards

On Tue, Jun 26, 2018 at 6:38 PM Devyani Samantarai <dev...@gm...>
wrote:

> Hi,
> I was tying out the nucmer function of Mummer, but  have problem plotting
> it. I wanted to plot a identity plot, like the one plotted in Fig 3 of this
> paper -
> https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-291#Fig3
> I tried using the mummerplot function, but the resulting plots are not
> like the one in the paper. Additionally I have some errors too.
>
> If you can kindly help, I will let you know the details.
>
> Thank you
> Regards
>
> --
> Devyani Samantarrai (PhD)
>
>

-- 
Devyani Samantarrai (PhD)

Dear Professor,

Excause me. I had run "dnadiff reference.fasta reads.fasta corrected" and then some error occured. The error is as following:

Building alignments
Filtering alignments
Extracting alignment coordinates
Analyzing SNPs
ERROR: Query input does not match delta file
ERROR: Failed to run show-snps, aborting.

And I had looked up the information on the internet,but there had no appropriate answer. Could you help me solve this problem?

Thanks.

Best wishes

Zahrah Sun
Hi Jorge,
It is likely that the input is misformatted in some way (e.g. the same
fasta header ID occurring multiple times). Check that your input fasta
files are correctly formatted.

Also, there is a new mummer release that should be more robust to such
parsing errors: https://mummer4.github.io

The output should be identical to mummer3.

Best,
-Adam

On Fri, Apr 6, 2018 at 6:30 AM, Jorge Chiapella <
jor...@un...> wrote:

> Hello Mummer-help
>
> I am trying to run basic Mummer to compare two sequences
> (antarctica=reference; cespitosa=query) and am getting this error "could
> not parse input from 'Query file'. Please check the filename and format".
>
>
> jorge@jorge:~/MUMmer3.23$ nucmer --maxgap=500 --mincluster=100
> --prefix=antarctica_cespitosa antarctica.fasta cespitosa.fasta
> 1: PREPARING DATA
> 2,3: RUNNING mummer AND CREATING CLUSTERS
> # reading input file "antarctica_cespitosa.ntref" of length 135363
> # construct suffix tree for sequence of length 135363
> # (maximum reference length is 536870908)
> # (maximum query length is 4294967295)
> # process 1353 characters per dot
> #...........................................................
> .........................................
> # CONSTRUCTIONTIME /usr/bin/mummer antarctica_cespitosa.ntref 0.04
> # reading input file "/home/jorge/MUMmer3.23/cespitosa.fasta" of length
> 135392
> # matching query-file "/home/jorge/MUMmer3.23/cespitosa.fasta"
> # against subject-file "antarctica_cespitosa.ntref"
> # COMPLETETIME /usr/bin/mummer antarctica_cespitosa.ntref 0.10
> # SPACE /usr/bin/mummer antarctica_cespitosa.ntref 0.26
> 4: FINISHING DATA
> ERROR: Could not parse input from 'Query File'.
> Please check the filename and format, or file a bug report
> ERROR: postnuc returned non-zero
>
>
>
> File format is OK, a normal Fasta. Have tried changing the Name -nothing.
> Have made a check as suggested after installing -nothing weird.
>
> jorge@jorge:~/MUMmer3.23$ make check
> check complete
> jorge@jorge:~/MUMmer3.23$
>
>
> Please some comment. Really need to use this tool.
>
> Thanks!
> Jorge
>
>
> --
> Jorge Chiapella
> Department of Botany and Biodiversity Research
> Faculty of Life Sciences
> University of Vienna
> Rennweg 14
> A-1020 Vienna
> AUSTRIA
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>

Hello Mummer-help

I am trying to run basic Mummer to compare two sequences 
(antarctica=reference; cespitosa=query) and am getting this error "could 
not parse input from 'Query file'. Please check the filename and 
format".

jorge@jorge:~/MUMmer3.23$ nucmer --maxgap=500 --mincluster=100 
--prefix=antarctica_cespitosa antarctica.fasta cespitosa.fasta
1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "antarctica_cespitosa.ntref" of length 135363
# construct suffix tree for sequence of length 135363
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 1353 characters per dot
#....................................................................................................
# CONSTRUCTIONTIME /usr/bin/mummer antarctica_cespitosa.ntref 0.04
# reading input file "/home/jorge/MUMmer3.23/cespitosa.fasta" of length 
135392
# matching query-file "/home/jorge/MUMmer3.23/cespitosa.fasta"
# against subject-file "antarctica_cespitosa.ntref"
# COMPLETETIME /usr/bin/mummer antarctica_cespitosa.ntref 0.10
# SPACE /usr/bin/mummer antarctica_cespitosa.ntref 0.26
4: FINISHING DATA
ERROR: Could not parse input from 'Query File'.
Please check the filename and format, or file a bug report
ERROR: postnuc returned non-zero

File format is OK, a normal Fasta. Have tried changing the Name 
-nothing. Have made a check as suggested after installing -nothing 
weird.

jorge@jorge:~/MUMmer3.23$ make check
check complete
jorge@jorge:~/MUMmer3.23$

Please some comment. Really need to use this tool.

Thanks!
Jorge

-- 
Jorge Chiapella
Department of Botany and Biodiversity Research
Faculty of Life Sciences
University of Vienna
Rennweg 14
A-1020 Vienna
AUSTRIA

Hi,

I am using Mummer to find if there is inversion happening between two
bacterial samples and have posted follwing question regarding Mummer in
biostarts.Can someone please have a look?

https://www.biostars.org/p/305288/#305294

I am trying to find if there is inversion happening between two bacterial
samples. I did the denovo assembly for the samples and then compared the
assemblies using Mummer.

Below is the graph that I got from Mummer. Please note that -r was used
while running mummer so that only reverse complement matches are shown. The
graph contains quite a few long lines with slope of -1 which means presence
of an inverted segment of conservation between the two sequences. The exact
mummer command used is as follows.

mummer -mum -F -r -c -l 100 ref.fasta query.fasta > output.mums

Mummer graph link: https://ibb.co/cQucnx

I manually checked the denovo assemblies for the regions highlighted by the
mums output file and indeed reverse complement is happening.

Some of the reverse matches shown in mums output file are really big in
size (some are about 330000 bp longs) and so the reverse match can not just
be a coincidence. The pipeline I have followed to generate denovo
assemblies is good one with only high quality reads selected for denovo.

Also just to add that reverse matches are are not complete contigs
(otherwise reverse matches could simply be down to assembler outputting in
reverse compliment for one of the contigs). For example below is a snippet
of mummer output showing two reverse matches. As can be seen contig 2 in
query sequence is of length 571230 bp but the reverse match is only of
length 339098. Similarly the contig 7 in query sequence is of length 327356
bp but there are only two reverse match for it in reference sequence of
lengths 42974 and 28669.

>NODE_2_QUERY_SEQ_length_571230_cov_70.7093 Reverse

NODE_5_REF_SEQ_length_339168_cov_61.2129 71 339098 339098
NODE_7_QUERY_SEQ_length_327356_cov_54.2118 Reverse

>NODE_25_REF_SEQ_length_71644_cov_64.1254 1 327356 42974

NODE_25_REF_SEQ_length_71644_cov_64.1254 42976 284381 28669
My questions are as follows:

The reverse matches are reverse complement matches (and not just reverse).
So basically Reverse complement of a subsequence in sample 1 exactly
matches with the corresponding subsequence in sample 2. My understanding is
that inverse mutation means reverse complement and not reverse. Let me know
if this is not correct.

In order to conclusive prove that there is indeed inverse mutations
happening between two samples, is the output from Mummer sufficient (which
is basically a mums file showing position in the reference sequence, the
position in the query sequence, and the length of the match for each
reverse match and a graph)? Of course we would again sequence to see if
same behaviour is repeated but as far as current sequence data is concerned
is there something else I can do to find our if inversion is present?

The next step will be to find the genes present in the reverse mutation
regions but please let me know if there is some else that I should consider.

Thanks for reading,

Cheers,
Ambi.
-- 

*This information is classified as confidential unless otherwise stated.*

This e-mail message is confidential and intended only for the addressee.
Unless you are the named addressee (or authorised to receive it for the
addressee) you may not copy or use it, or disclose it to anyone else. If
the message is received by anyone other than the addressee, please return
the message to the sender by replying to it and then delete the message
from your computer.

Hi Adam and other MUMmer support team,

I attached a screenshot of mummerplot output. There are some thick lines and some thin ones. I am wondering if those thick lines are clusters of start and end of each hit (which are represented by dots) and thin lines are the long alignments which are represented by lines. 

Besides of ps output format, could it be other higher resolution format like svg, which I could zoom it to see more details of whether are are gaps between some alignments?

Thank you
Qihua

> On Dec 11, 2017, at 1:46 PM, Adam Phillippy <aph...@gm...> wrote:
> 
> Not unusual. If you zoom in on the interactive plot (right mouse button) you should be able to see what's happening. Likely to be small, in-place inversions w/in contigs or at the ends of contigs.
> 
> On Mon, Dec 11, 2017 at 4:43 PM, Qihua Liang <qli...@uc... <mailto:qli...@uc...>> wrote:
> Hi Adam,
> 
> What about blue plots aligning on the diagonal? I attached a figure and it looks like blue and red are both aligning along the diagonal. I think the blue one should from the other diagonal?
> 
> Thank you
> Qihua
> 
> <PastedGraphic-1.png>
> 
> 
>> On Dec 11, 2017, at 12:39 PM, Adam Phillippy <aph...@gm... <mailto:aph...@gm...>> wrote:
>> 
>> Yes, red are forward-strand matches and blue are reverse. Large stretches of blue would indicate inversions, though smaller ones may just be repetitive matches.
>> 
>> Best,
>> -Adam
>> 
>> On Mon, Dec 11, 2017 at 3:29 PM, Qihua Liang <qli...@uc... <mailto:qli...@uc...>> wrote:
>> Hi Adam,
>> 
>> Thank you for your advice on -l. It works great with generating the diagonal plot.
>> 
>> But it is confusing that the diagonal plot seems to have both red and blue color on it. I think it means both forward and reverse matches on the same position, but why would that happen?
>> 
>> Thanks
>> Qihua
>> 
>>> On Nov 29, 2017, at 12:34 PM, Adam Phillippy <aph...@gm... <mailto:aph...@gm...>> wrote:
>>> 
>>> Hi Qihua,
>>> Try adding the --layout or --fat options and mummerplot will arrange and orient the contigs to make things look better.
>>> 
>>> Best,
>>> -Adam
>>> 
>>> On Mon, Nov 27, 2017 at 4:28 AM, Qihua Liang <qli...@uc... <mailto:qli...@uc...>> wrote:
>>> Dear MUMmer develop team,
>>> 
>>> I am trying to use NUCmer together with mummer plot to compare different assemblies of the same plant genome (~640Mb) and my command is:
>>> nucmer --maxmatch -l 100 -c 100 -p compare1_2 assembly1.fasta assembly2.fasta
>>> mummerplot --png -p compare1_2 compare1_2.delta -R assembly1.fasta -Q assembly2.fasta
>>> 
>>> Both assemblies have hundreds of contigs, and thus the figure looks messy. Could you provide some instructions on tuning the parameters to better generate dot plot for two draft assemblies on contig level?
>>> 
>>> Thank you so much
>>> Qihua
>>> 
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot <http://sdm.link/slashdot>
>>> _______________________________________________
>>> MUMmer-help mailing list
>>> MUM...@li... <mailto:MUM...@li...>
>>> https://lists.sourceforge.net/lists/listinfo/mummer-help <https://lists.sourceforge.net/lists/listinfo/mummer-help>
>>> 
>>> 
>> 
>> 
> 
> 

Thank you, Manish!

Last time the job was killed since the computation time I set wasn't
enough. I just checked my .delta result after successful running.  I'm
still confused. Although I can see there is match in chr.1 from nucmer
--maxmatch, the match regions are short. (even shorter than the result from
nucmer) Still didn't see the result like I blat. ( If I simply blat the
sequence of Scaffold18596 to the same reference genome, I found there're
several perfect matches in chr.1 (11,360 bp, 3,618 bp, 2,445 bp).)

"nuc.out.delta" is the output from nucmer.
[image: Inline image 1]

"sample1.MH.maxmatch.delta" is the output from nucmer --maxmatch

[image: Inline image 2]

Thank you very much!!
Yuya

On Mon, Feb 5, 2018 at 10:52 AM, Manish Goel <go...@mp...> wrote:

> Hi,
>
> No, from my experience I would say that it didn't finish properly. Did you
> check the output and error files?
>
> Best
> Manish
>
> On 02/05/2018 05:27 PM, Yu-Ya Liang wrote:
>
> Hi Manish,
>
> Thank you for the reply!
>
> My `nucmer` job just finished but I can’t find .delta output file. Is that
> normal? (I didn’t get any .delta file after this job.) I only got
> "sample1.MH.max.mgaps” and “sample1.MH.max.ntref” two output.
>
>
>
>
> Best regards,
> Yuya
>
>
>
>
> On Feb 4, 2018, at 1:54 AM, manish goel <go...@mp...> wrote:
>
> Hi,
>
> The option is --maxmatch (not -maxmatch).
>
> Best
> Manish
>
>
> *From: *Yu-Ya Liang <r02...@ta...>
> *Sent: *04 February 2018 03:26
> *To: *Adam Phillippy <aph...@gm...>; MUMmer-help@lists.
> sourceforge.net
> *Subject: *Re: [MUMmer-help] Question: result in "blat" and "nucmer"
> aredifferent?
>
> Hi Adam,
>
> Thank you for rapid reply! I submitted my job with -maxmatch option but
> the result still same. I used `grep` to check where Scaffold18596 located.
> The result is exact same as my previous result, which without adding
> -maxmatch.
>
>
> Do you happen to know what's going on with my command?
>
> Here's the command I used:
> [r02621109@ada4 rice_asmbl]$ more nucmer.bsub
> #!/bin/bash
>
> #BSUB -W 10:00 # wall-clock time
> #BSUB -L /bin/bash
> #BSUB -n 10
> #BSUB -R "span[ptile=10]"
> #BSUB -R "rusage[mem=2000]"
> #BSUB -J NUC[1]
> #BSUB -o NUC.%J.%I.out
> #BSUB -e NUC.%J.%I.err
>
> module load MUMmer/3.23-intel-2015B
>
>
> date
>
> echo "nucmer /home/r02621109/scratch/rice_ref/MH63RS1.LNNK00000000.fsa.fa
> /home/r02621109/scratch/rice_asmbl/K63/sample${LSB_JOBINDEX}_asmbl.scafS
> eq"
>
> nucmer -maxmatch -p sample1.MH.max /home/r02621109/scratch/rice_
> ref/MH63RS1.LNNK00000000.fsa.fa /home/r02621109/scratch/rice_
> asmbl/K63/sample1_asm
> bl.scafSeq
>
>
> date
>
>
> Thank you very much!!
> Yuya
>
>
> On Sat, Feb 3, 2018 at 7:42 AM, Adam Phillippy <aph...@gm...>
> wrote:
>
> Hi Yuya,
> Add the -maxmatch option and it should find all the matches. It uses only
> unique anchor sequences in the reference by default, which can cause
> duplicate matches to be missed.
>
> Best,
> Adam
>
> Sent from my mobile.
>
>
> On Feb 2, 2018, at 11:50 PM, Yu-Ya Liang <r02...@ta...> wrote:
>
> Hi,
>
> Thank you for developing such good tool! I'm using MUMmer3 for my genome
> assembly project. I have a question regarding  nucmer function.
>
>
> I used nucmerto align each scaffold to chromosome based on the reference
> genome.
>
> After nucmer alignment, Scaffold18596 is located in chr.5 (only 530 bp
> match chr.5 but it's the highest score). However, if I simply blat the
> sequence of Scaffold18596 to the same reference genome, I found there're
> several perfect matches in chr.1 (11,360 bp, 3,618 bp, 2,445 bp).
>
> In this case, why nucmer gave me this strange result? For the command, I
> just simply used nucmer -p <Reference> <Query>
>
>
>
> Did I do something wrong?
>
>
>
> Best regards,
>
> Yuya
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__Slashdot.org&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=XVGA-sMt2CytLihcf0l5tBeLzY_2M8VBkNCFF2gEH-k&m=fszAuFxlQy9wqLom4uMaGFCx4-DlzcCjT7S5dVAZDwc&s=Z8xJwjRSObGxMj-O0D-Ochra5iBAbbGQ15ENs-8fmFA&e=>
> ! http://sdm.link/slashdot
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=XVGA-sMt2CytLihcf0l5tBeLzY_2M8VBkNCFF2gEH-k&m=fszAuFxlQy9wqLom4uMaGFCx4-DlzcCjT7S5dVAZDwc&s=nd4Wd5EbA_6Jg2egNWdw1EOWv_flS-rA7sKxMqp4DM8&e=>
>
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_mummer-2Dhelp&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=XVGA-sMt2CytLihcf0l5tBeLzY_2M8VBkNCFF2gEH-k&m=fszAuFxlQy9wqLom4uMaGFCx4-DlzcCjT7S5dVAZDwc&s=P3l3EuY43AE7UBv4wSUne5M9f_0Z8yhkpbY_95zJVSM&e=>
>
>
>
>

Hi Manish,

Thank you for the reply! 

My `nucmer` job just finished but I can’t find .delta output file. Is that normal? (I didn’t get any .delta file after this job.) I only got "sample1.MH.max.mgaps” and “sample1.MH.max.ntref” two output.

Best regards,
Yuya

> On Feb 4, 2018, at 1:54 AM, manish goel <go...@mp...> wrote:
> 
> Hi,
>  
> The option is --maxmatch (not -maxmatch).
>  
> Best
> Manish
>  
>  
> From: Yu-Ya Liang <mailto:r02...@ta...>
> Sent: 04 February 2018 03:26
> To: Adam Phillippy <mailto:aph...@gm...>; MUM...@li... <mailto:MUM...@li...>
> Subject: Re: [MUMmer-help] Question: result in "blat" and "nucmer" aredifferent?
>  
> Hi Adam,
>  
> Thank you for rapid reply! I submitted my job with -maxmatch option but the result still same. I used `grep` to check where Scaffold18596 located. The result is exact same as my previous result, which without adding -maxmatch. 
>  
>  
> Do you happen to know what's going on with my command?
>  
> Here's the command I used: 
> [r02621109@ada4 rice_asmbl]$ more nucmer.bsub
> #!/bin/bash
>  
> #BSUB -W 10:00 # wall-clock time
> #BSUB -L /bin/bash
> #BSUB -n 10
> #BSUB -R "span[ptile=10]"
> #BSUB -R "rusage[mem=2000]"
> #BSUB -J NUC[1]
> #BSUB -o NUC.%J.%I.out
> #BSUB -e NUC.%J.%I.err
>  
> module load MUMmer/3.23-intel-2015B
>  
>  
> date
>  
> echo "nucmer /home/r02621109/scratch/rice_ref/MH63RS1.LNNK00000000.fsa.fa /home/r02621109/scratch/rice_asmbl/K63/sample${LSB_JOBINDEX}_asmbl.scafS
> eq"
>  
> nucmer -maxmatch -p sample1.MH.max /home/r02621109/scratch/rice_ref/MH63RS1.LNNK00000000.fsa.fa /home/r02621109/scratch/rice_asmbl/K63/sample1_asm
> bl.scafSeq
>  
>  
> date
>  
>  
> Thank you very much!!
> Yuya
>  
>  
> On Sat, Feb 3, 2018 at 7:42 AM, Adam Phillippy <aph...@gm... <mailto:aph...@gm...>> wrote:
> Hi Yuya,
> Add the -maxmatch option and it should find all the matches. It uses only unique anchor sequences in the reference by default, which can cause duplicate matches to be missed.
>  
> Best,
> Adam
>  
> Sent from my mobile.
> 
> On Feb 2, 2018, at 11:50 PM, Yu-Ya Liang <r02...@ta... <mailto:r02...@ta...>> wrote:
> 
> Hi,
>  
> Thank you for developing such good tool! I'm using MUMmer3 for my genome assembly project. I have a question regarding  nucmer function. 
>  
> I used nucmerto align each scaffold to chromosome based on the reference genome.
> 
> After nucmer alignment, Scaffold18596 is located in chr.5 (only 530 bp match chr.5 but it's the highest score). However, if I simply blat the sequence of Scaffold18596 to the same reference genome, I found there're several perfect matches in chr.1 (11,360 bp, 3,618 bp, 2,445 bp). 
> 
> In this case, why nucmer gave me this strange result? For the command, I just simply used nucmer -p <Reference> <Query>
> 
>  
> 
> Did I do something wrong?
> 
>  
> 
> Best regards,
> 
> Yuya
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org <https://urldefense.proofpoint.com/v2/url?u=http-3A__Slashdot.org&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=XVGA-sMt2CytLihcf0l5tBeLzY_2M8VBkNCFF2gEH-k&m=fszAuFxlQy9wqLom4uMaGFCx4-DlzcCjT7S5dVAZDwc&s=Z8xJwjRSObGxMj-O0D-Ochra5iBAbbGQ15ENs-8fmFA&e=>! http://sdm.link/slashdot <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=XVGA-sMt2CytLihcf0l5tBeLzY_2M8VBkNCFF2gEH-k&m=fszAuFxlQy9wqLom4uMaGFCx4-DlzcCjT7S5dVAZDwc&s=nd4Wd5EbA_6Jg2egNWdw1EOWv_flS-rA7sKxMqp4DM8&e=>
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li... <mailto:MUM...@li...>
> https://lists.sourceforge.net/lists/listinfo/mummer-help <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_mummer-2Dhelp&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=XVGA-sMt2CytLihcf0l5tBeLzY_2M8VBkNCFF2gEH-k&m=fszAuFxlQy9wqLom4uMaGFCx4-DlzcCjT7S5dVAZDwc&s=P3l3EuY43AE7UBv4wSUne5M9f_0Z8yhkpbY_95zJVSM&e=>

Hi,

No, from my experience I would say that it didn't finish properly. Did 
you check the output and error files?

Best
Manish

On 02/05/2018 05:27 PM, Yu-Ya Liang wrote:
> Hi Manish,
>
> Thank you for the reply!
>
> My `nucmer` job just finished but I can’t find .delta output file. Is 
> that normal? (I didn’t get any .delta file after this job.) I only got 
> "sample1.MH.max.mgaps” and “sample1.MH.max.ntref” two output.
>
>
>
>
> Best regards,
> Yuya
>
>
>
>
>> On Feb 4, 2018, at 1:54 AM, manish goel <go...@mp... 
>> <mailto:go...@mp...>> wrote:
>>
>> Hi,
>> The option is --maxmatch (not -maxmatch).
>> Best
>> Manish
>> *From:*Yu-Ya Liang <mailto:r02...@ta...>
>> *Sent:*04 February 2018 03:26
>> *To:*Adam Phillippy 
>> <mailto:aph...@gm...>;MUM...@li... 
>> <mailto:MUM...@li...>
>> *Subject:*Re: [MUMmer-help] Question: result in "blat" and "nucmer" 
>> aredifferent?
>> Hi Adam,
>> Thank you for rapid reply! I submitted my job with -maxmatch option 
>> but the result still same. I used `grep` to check where Scaffold18596 
>> located. The result is exact same as my previous result, which 
>> without adding -maxmatch.
>> Do you happen to know what's going on with my command?
>> Here's the command I used:
>> [r02621109@ada4 rice_asmbl]$ more nucmer.bsub
>> #!/bin/bash
>> #BSUB -W 10:00 # wall-clock time
>> #BSUB -L /bin/bash
>> #BSUB -n 10
>> #BSUB -R "span[ptile=10]"
>> #BSUB -R "rusage[mem=2000]"
>> #BSUB -J NUC[1]
>> #BSUB -o NUC.%J.%I.out
>> #BSUB -e NUC.%J.%I.err
>> module load MUMmer/3.23-intel-2015B
>> date
>> echo "nucmer 
>> /home/r02621109/scratch/rice_ref/MH63RS1.LNNK00000000.fsa.fa 
>> /home/r02621109/scratch/rice_asmbl/K63/sample${LSB_JOBINDEX}_asmbl.scafS
>> eq"
>> nucmer -maxmatch -p sample1.MH.max 
>> /home/r02621109/scratch/rice_ref/MH63RS1.LNNK00000000.fsa.fa 
>> /home/r02621109/scratch/rice_asmbl/K63/sample1_asm
>> bl.scafSeq
>> date
>> Thank you very much!!
>> Yuya
>> On Sat, Feb 3, 2018 at 7:42 AM, Adam Phillippy <aph...@gm... 
>> <mailto:aph...@gm...>> wrote:
>>
>>     Hi Yuya,
>>     Add the -maxmatch option and it should find all the matches. It
>>     uses only unique anchor sequences in the reference by default,
>>     which can cause duplicate matches to be missed.
>>     Best,
>>     Adam
>>     Sent from my mobile.
>>
>>
>>     On Feb 2, 2018, at 11:50 PM, Yu-Ya Liang <r02...@ta...
>>     <mailto:r02...@ta...>> wrote:
>>
>>         Hi,
>>         Thank you for developing such good tool! I'm using MUMmer3
>>         for my genome assembly project. I have a question regarding
>>         |nucmer| function.
>>
>>         I used |nucmer|to align each scaffold to chromosome based on
>>         the reference genome.
>>
>>         After |nucmer| alignment, Scaffold18596 is located in chr.5
>>         (only 530 bp match chr.5 but it's the highest score).
>>         However, if I simply |blat| the sequence of Scaffold18596 to
>>         the same reference genome, I found there're several perfect
>>         matches in chr.1 (11,360 bp, 3,618 bp, 2,445 bp).
>>
>>         In this case, why |nucmer| gave me this strange result? For
>>         the command, I just simply used |nucmer -p <Reference> <Query>|
>>
>>         Did I do something wrong?
>>
>>         Best regards,
>>
>>         Yuya
>>
>>         ------------------------------------------------------------------------------
>>         Check out the vibrant tech community on one of the world's most
>>         engaging tech sites,Slashdot.org
>>         <https://urldefense.proofpoint.com/v2/url?u=http-3A__Slashdot.org&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=XVGA-sMt2CytLihcf0l5tBeLzY_2M8VBkNCFF2gEH-k&m=fszAuFxlQy9wqLom4uMaGFCx4-DlzcCjT7S5dVAZDwc&s=Z8xJwjRSObGxMj-O0D-Ochra5iBAbbGQ15ENs-8fmFA&e=>!http://sdm.link/slashdot
>>         <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=XVGA-sMt2CytLihcf0l5tBeLzY_2M8VBkNCFF2gEH-k&m=fszAuFxlQy9wqLom4uMaGFCx4-DlzcCjT7S5dVAZDwc&s=nd4Wd5EbA_6Jg2egNWdw1EOWv_flS-rA7sKxMqp4DM8&e=>
>>
>>         _______________________________________________
>>         MUMmer-help mailing list
>>         MUM...@li...
>>         <mailto:MUM...@li...>
>>         https://lists.sourceforge.net/lists/listinfo/mummer-help
>>         <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_mummer-2Dhelp&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=XVGA-sMt2CytLihcf0l5tBeLzY_2M8VBkNCFF2gEH-k&m=fszAuFxlQy9wqLom4uMaGFCx4-DlzcCjT7S5dVAZDwc&s=P3l3EuY43AE7UBv4wSUne5M9f_0Z8yhkpbY_95zJVSM&e=>
>>
>

Hi,

The option is --maxmatch (not -maxmatch).

Best
Manish

From: Yu-Ya Liang
Sent: 04 February 2018 03:26
To: Adam Phillippy; MUM...@li...
Subject: Re: [MUMmer-help] Question: result in "blat" and "nucmer" aredifferent?

Hi Adam,

Thank you for rapid reply! I submitted my job with -maxmatch option but the result still same. I used `grep` to check where Scaffold18596 located. The result is exact same as my previous result, which without adding -maxmatch. 

Do you happen to know what's going on with my command?

Here's the command I used: 
[r02621109@ada4 rice_asmbl]$ more nucmer.bsub
#!/bin/bash

#BSUB -W 10:00 # wall-clock time
#BSUB -L /bin/bash
#BSUB -n 10
#BSUB -R "span[ptile=10]"
#BSUB -R "rusage[mem=2000]"
#BSUB -J NUC[1]
#BSUB -o NUC.%J.%I.out
#BSUB -e NUC.%J.%I.err

module load MUMmer/3.23-intel-2015B

date

echo "nucmer /home/r02621109/scratch/rice_ref/MH63RS1.LNNK00000000.fsa.fa /home/r02621109/scratch/rice_asmbl/K63/sample${LSB_JOBINDEX}_asmbl.scafS
eq"

nucmer -maxmatch -p sample1.MH.max /home/r02621109/scratch/rice_ref/MH63RS1.LNNK00000000.fsa.fa /home/r02621109/scratch/rice_asmbl/K63/sample1_asm
bl.scafSeq

date

Thank you very much!!
Yuya

On Sat, Feb 3, 2018 at 7:42 AM, Adam Phillippy <aph...@gm...> wrote:
Hi Yuya,
Add the -maxmatch option and it should find all the matches. It uses only unique anchor sequences in the reference by default, which can cause duplicate matches to be missed.

Best,
Adam

Sent from my mobile.

On Feb 2, 2018, at 11:50 PM, Yu-Ya Liang <r02...@ta...> wrote:
Hi,

Thank you for developing such good tool! I'm using MUMmer3 for my genome assembly project. I have a question regarding  nucmer function. 

I used nucmerto align each scaffold to chromosome based on the reference genome.
After nucmer alignment, Scaffold18596 is located in chr.5 (only 530 bp match chr.5 but it's the highest score). However, if I simply blat the sequence of Scaffold18596 to the same reference genome, I found there're several perfect matches in chr.1 (11,360 bp, 3,618 bp, 2,445 bp). 
In this case, why nucmer gave me this strange result? For the command, I just simply used nucmer -p <Reference> <Query>

Did I do something wrong?

Best regards,
Yuya
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
MUMmer-help mailing list
MUM...@li...
https://lists.sourceforge.net/lists/listinfo/mummer-help

Hi Adam,

Thank you for rapid reply! I submitted my job with -maxmatch option but the
result still same. I used `grep` to check where Scaffold18596 located. The
result is exact same as my previous result, which without adding -maxmatch.

Do you happen to know what's going on with my command?

Here's the command I used:

[r02621109@ada4 rice_asmbl]$ more nucmer.bsub

#!/bin/bash

#BSUB -W 10:00 # wall-clock time

#BSUB -L /bin/bash

#BSUB -n 10

#BSUB -R "span[ptile=10]"

#BSUB -R "rusage[mem=2000]"

#BSUB -J NUC[1]

#BSUB -o NUC.%J.%I.out

#BSUB -e NUC.%J.%I.err

module load MUMmer/3.23-intel-2015B

date

echo "nucmer /home/r02621109/scratch/rice_ref/MH63RS1.LNNK00000000.fsa.fa
/home/r02621109/scratch/rice_asmbl/K63/sample${LSB_JOBINDEX}_asmbl.scafS

eq"

nucmer -maxmatch -p sample1.MH.max
/home/r02621109/scratch/rice_ref/MH63RS1.LNNK00000000.fsa.fa
/home/r02621109/scratch/rice_asmbl/K63/sample1_asm

bl.scafSeq

date

Thank you very much!!
Yuya

On Sat, Feb 3, 2018 at 7:42 AM, Adam Phillippy <aph...@gm...> wrote:

> Hi Yuya,
> Add the -maxmatch option and it should find all the matches. It uses only
> unique anchor sequences in the reference by default, which can cause
> duplicate matches to be missed.
>
> Best,
> Adam
>
> Sent from my mobile.
>
> On Feb 2, 2018, at 11:50 PM, Yu-Ya Liang <r02...@ta...> wrote:
>
> Hi,
>
> Thank you for developing such good tool! I'm using MUMmer3 for my genome
> assembly project. I have a question regarding  nucmer function.
>
> I used nucmerto align each scaffold to chromosome based on the reference
> genome.
>
> After nucmer alignment, Scaffold18596 is located in chr.5 (only 530 bp
> match chr.5 but it's the highest score). However, if I simply blat the
> sequence of Scaffold18596 to the same reference genome, I found there're
> several perfect matches in chr.1 (11,360 bp, 3,618 bp, 2,445 bp).
>
> In this case, why nucmer gave me this strange result? For the command, I
> just simply used nucmer -p <Reference> <Query>
>
>
> Did I do something wrong?
>
>
> Best regards,
>
> Yuya
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__Slashdot.org&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=XVGA-sMt2CytLihcf0l5tBeLzY_2M8VBkNCFF2gEH-k&m=fszAuFxlQy9wqLom4uMaGFCx4-DlzcCjT7S5dVAZDwc&s=Z8xJwjRSObGxMj-O0D-Ochra5iBAbbGQ15ENs-8fmFA&e=>!
> http://sdm.link/slashdot
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=XVGA-sMt2CytLihcf0l5tBeLzY_2M8VBkNCFF2gEH-k&m=fszAuFxlQy9wqLom4uMaGFCx4-DlzcCjT7S5dVAZDwc&s=nd4Wd5EbA_6Jg2egNWdw1EOWv_flS-rA7sKxMqp4DM8&e=>
>
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_mummer-2Dhelp&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=XVGA-sMt2CytLihcf0l5tBeLzY_2M8VBkNCFF2gEH-k&m=fszAuFxlQy9wqLom4uMaGFCx4-DlzcCjT7S5dVAZDwc&s=P3l3EuY43AE7UBv4wSUne5M9f_0Z8yhkpbY_95zJVSM&e=>
>
>

Hi Yuya,
Add the -maxmatch option and it should find all the matches. It uses only unique anchor sequences in the reference by default, which can cause duplicate matches to be missed.

Best,
Adam

Sent from my mobile.

> On Feb 2, 2018, at 11:50 PM, Yu-Ya Liang <r02...@ta...> wrote:
> 
> Hi,
> 
> Thank you for developing such good tool! I'm using MUMmer3 for my genome assembly project. I have a question regarding  nucmer function. 
> 
> I used nucmerto align each scaffold to chromosome based on the reference genome.
> 
> After nucmer alignment, Scaffold18596 is located in chr.5 (only 530 bp match chr.5 but it's the highest score). However, if I simply blat the sequence of Scaffold18596 to the same reference genome, I found there're several perfect matches in chr.1 (11,360 bp, 3,618 bp, 2,445 bp). 
> 
> In this case, why nucmer gave me this strange result? For the command, I just simply used nucmer -p <Reference> <Query>
> 
> 
> 
> Did I do something wrong?
> 
> 
> 
> Best regards,
> 
> Yuya
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help

Hi,

Thank you for developing such good tool! I'm using MUMmer3 for my genome
assembly project. I have a question regarding  nucmer function.

I used nucmerto align each scaffold to chromosome based on the reference
genome.

After nucmer alignment, Scaffold18596 is located in chr.5 (only 530 bp
match chr.5 but it's the highest score). However, if I simply blat the
sequence of Scaffold18596 to the same reference genome, I found there're
several perfect matches in chr.1 (11,360 bp, 3,618 bp, 2,445 bp).

In this case, why nucmer gave me this strange result? For the command, I
just simply used nucmer -p <Reference> <Query>

Did I do something wrong?

Best regards,

Yuya

Dear MUMmer Develop Team,

I am comparing two different assemblies of the same species (same accessions too). The parameter I am using is: 
nucmer --maxmatch -l 1000 -c 2000

I am confused how -l (Minimum length of an maximal exact match) and -c (Minimum cluster length) works in producing a hit. -l 1000 is that an exact alignment should be >1kb, and what about -c 2000?

Since I am comparing two highly similar assemblies, do you have any suggestions on how or what parameters to tune?

Thank you
Qihua

Not unusual. If you zoom in on the interactive plot (right mouse button)
you should be able to see what's happening. Likely to be small, in-place
inversions w/in contigs or at the ends of contigs.

On Mon, Dec 11, 2017 at 4:43 PM, Qihua Liang <qli...@uc...> wrote:

> Hi Adam,
>
> What about blue plots aligning on the diagonal? I attached a figure and it
> looks like blue and red are both aligning along the diagonal. I think the
> blue one should from the other diagonal?
>
> Thank you
> Qihua
>
>
>
> On Dec 11, 2017, at 12:39 PM, Adam Phillippy <aph...@gm...> wrote:
>
> Yes, red are forward-strand matches and blue are reverse. Large stretches
> of blue would indicate inversions, though smaller ones may just be
> repetitive matches.
>
> Best,
> -Adam
>
> On Mon, Dec 11, 2017 at 3:29 PM, Qihua Liang <qli...@uc...> wrote:
>
>> Hi Adam,
>>
>> Thank you for your advice on -l. It works great with generating the
>> diagonal plot.
>>
>> But it is confusing that the diagonal plot seems to have both red and
>> blue color on it. I think it means both forward and reverse matches on the
>> same position, but why would that happen?
>>
>> Thanks
>> Qihua
>>
>> On Nov 29, 2017, at 12:34 PM, Adam Phillippy <aph...@gm...>
>> wrote:
>>
>> Hi Qihua,
>> Try adding the --layout or --fat options and mummerplot will arrange and
>> orient the contigs to make things look better.
>>
>> Best,
>> -Adam
>>
>> On Mon, Nov 27, 2017 at 4:28 AM, Qihua Liang <qli...@uc...> wrote:
>>
>>> Dear MUMmer develop team,
>>>
>>> I am trying to use NUCmer together with mummer plot to compare different
>>> assemblies of the same plant genome (~640Mb) and my command is:
>>> nucmer --maxmatch -l 100 -c 100 -p compare1_2 assembly1.fasta
>>> assembly2.fasta
>>> mummerplot --png -p compare1_2 compare1_2.delta -R assembly1.fasta
>>> -Q assembly2.fasta
>>>
>>> Both assemblies have hundreds of contigs, and thus the figure looks
>>> messy. Could you provide some instructions on tuning the parameters to
>>> better generate dot plot for two draft assemblies on contig level?
>>>
>>> Thank you so much
>>> Qihua
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org <http://slashdot.org/>!
>>> http://sdm.link/slashdot
>>> _______________________________________________
>>> MUMmer-help mailing list
>>> MUM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/mummer-help
>>>
>>>
>>
>>
>
>

Hi Adam,

What about blue plots aligning on the diagonal? I attached a figure and it looks like blue and red are both aligning along the diagonal. I think the blue one should from the other diagonal?

Thank you
Qihua

> On Dec 11, 2017, at 12:39 PM, Adam Phillippy <aph...@gm...> wrote:
> 
> Yes, red are forward-strand matches and blue are reverse. Large stretches of blue would indicate inversions, though smaller ones may just be repetitive matches.
> 
> Best,
> -Adam
> 
> On Mon, Dec 11, 2017 at 3:29 PM, Qihua Liang <qli...@uc... <mailto:qli...@uc...>> wrote:
> Hi Adam,
> 
> Thank you for your advice on -l. It works great with generating the diagonal plot.
> 
> But it is confusing that the diagonal plot seems to have both red and blue color on it. I think it means both forward and reverse matches on the same position, but why would that happen?
> 
> Thanks
> Qihua
> 
>> On Nov 29, 2017, at 12:34 PM, Adam Phillippy <aph...@gm... <mailto:aph...@gm...>> wrote:
>> 
>> Hi Qihua,
>> Try adding the --layout or --fat options and mummerplot will arrange and orient the contigs to make things look better.
>> 
>> Best,
>> -Adam
>> 
>> On Mon, Nov 27, 2017 at 4:28 AM, Qihua Liang <qli...@uc... <mailto:qli...@uc...>> wrote:
>> Dear MUMmer develop team,
>> 
>> I am trying to use NUCmer together with mummer plot to compare different assemblies of the same plant genome (~640Mb) and my command is:
>> nucmer --maxmatch -l 100 -c 100 -p compare1_2 assembly1.fasta assembly2.fasta
>> mummerplot --png -p compare1_2 compare1_2.delta -R assembly1.fasta -Q assembly2.fasta
>> 
>> Both assemblies have hundreds of contigs, and thus the figure looks messy. Could you provide some instructions on tuning the parameters to better generate dot plot for two draft assemblies on contig level?
>> 
>> Thank you so much
>> Qihua
>> 
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot <http://sdm.link/slashdot>
>> _______________________________________________
>> MUMmer-help mailing list
>> MUM...@li... <mailto:MUM...@li...>
>> https://lists.sourceforge.net/lists/listinfo/mummer-help <https://lists.sourceforge.net/lists/listinfo/mummer-help>
>> 
>> 
> 
> 

Yes, red are forward-strand matches and blue are reverse. Large stretches
of blue would indicate inversions, though smaller ones may just be
repetitive matches.

Best,
-Adam

On Mon, Dec 11, 2017 at 3:29 PM, Qihua Liang <qli...@uc...> wrote:

> Hi Adam,
>
> Thank you for your advice on -l. It works great with generating the
> diagonal plot.
>
> But it is confusing that the diagonal plot seems to have both red and blue
> color on it. I think it means both forward and reverse matches on the same
> position, but why would that happen?
>
> Thanks
> Qihua
>
> On Nov 29, 2017, at 12:34 PM, Adam Phillippy <aph...@gm...> wrote:
>
> Hi Qihua,
> Try adding the --layout or --fat options and mummerplot will arrange and
> orient the contigs to make things look better.
>
> Best,
> -Adam
>
> On Mon, Nov 27, 2017 at 4:28 AM, Qihua Liang <qli...@uc...> wrote:
>
>> Dear MUMmer develop team,
>>
>> I am trying to use NUCmer together with mummer plot to compare different
>> assemblies of the same plant genome (~640Mb) and my command is:
>> nucmer --maxmatch -l 100 -c 100 -p compare1_2 assembly1.fasta
>> assembly2.fasta
>> mummerplot --png -p compare1_2 compare1_2.delta -R assembly1.fasta
>> -Q assembly2.fasta
>>
>> Both assemblies have hundreds of contigs, and thus the figure looks
>> messy. Could you provide some instructions on tuning the parameters to
>> better generate dot plot for two draft assemblies on contig level?
>>
>> Thank you so much
>> Qihua
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org <http://slashdot.org>!
>> http://sdm.link/slashdot
>> _______________________________________________
>> MUMmer-help mailing list
>> MUM...@li...
>> https://lists.sourceforge.net/lists/listinfo/mummer-help
>>
>>
>
>

Hi Adam,

Thank you for your advice on -l. It works great with generating the diagonal plot.

But it is confusing that the diagonal plot seems to have both red and blue color on it. I think it means both forward and reverse matches on the same position, but why would that happen?

Thanks
Qihua

> On Nov 29, 2017, at 12:34 PM, Adam Phillippy <aph...@gm...> wrote:
> 
> Hi Qihua,
> Try adding the --layout or --fat options and mummerplot will arrange and orient the contigs to make things look better.
> 
> Best,
> -Adam
> 
> On Mon, Nov 27, 2017 at 4:28 AM, Qihua Liang <qli...@uc... <mailto:qli...@uc...>> wrote:
> Dear MUMmer develop team,
> 
> I am trying to use NUCmer together with mummer plot to compare different assemblies of the same plant genome (~640Mb) and my command is:
> nucmer --maxmatch -l 100 -c 100 -p compare1_2 assembly1.fasta assembly2.fasta
> mummerplot --png -p compare1_2 compare1_2.delta -R assembly1.fasta -Q assembly2.fasta
> 
> Both assemblies have hundreds of contigs, and thus the figure looks messy. Could you provide some instructions on tuning the parameters to better generate dot plot for two draft assemblies on contig level?
> 
> Thank you so much
> Qihua
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot <http://sdm.link/slashdot>
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li... <mailto:MUM...@li...>
> https://lists.sourceforge.net/lists/listinfo/mummer-help <https://lists.sourceforge.net/lists/listinfo/mummer-help>
> 
> 

2005	Jan	Feb	Mar	Apr	May (1)	Jun (2)	Jul (5)	Aug (3)	Sep (10)	Oct (9)	Nov (4)	Dec (3)
2006	Jan (5)	Feb (4)	Mar (19)	Apr (5)	May (10)	Jun (3)	Jul (5)	Aug (6)	Sep (8)	Oct (14)	Nov (9)	Dec (8)
2007	Jan (13)	Feb (6)	Mar (8)	Apr (3)	May (7)	Jun (5)	Jul (6)	Aug (15)	Sep (13)	Oct (7)	Nov (15)	Dec (15)
2008	Jan (7)	Feb (15)	Mar (12)	Apr (24)	May (25)	Jun (14)	Jul (36)	Aug (17)	Sep (26)	Oct (26)	Nov (24)	Dec (42)
2009	Jan (15)	Feb (18)	Mar (26)	Apr (41)	May (45)	Jun (4)	Jul (5)	Aug (3)	Sep (10)	Oct (12)	Nov (10)	Dec (3)
2010	Jan (16)	Feb (9)	Mar (5)	Apr (5)	May (3)	Jun (11)	Jul (9)	Aug (3)	Sep (18)	Oct (5)	Nov (2)	Dec (5)
2011	Jan (3)	Feb (10)	Mar (16)	Apr (3)	May (5)	Jun (22)	Jul (4)	Aug (6)	Sep (9)	Oct (6)	Nov (5)	Dec (6)
2012	Jan (2)	Feb (2)	Mar (4)	Apr (7)	May (2)	Jun (5)	Jul (6)	Aug (6)	Sep (8)	Oct (2)	Nov	Dec (5)
2013	Jan (11)	Feb (2)	Mar (1)	Apr (3)	May (4)	Jun (3)	Jul (1)	Aug (3)	Sep (2)	Oct (1)	Nov (3)	Dec (5)
2014	Jan (5)	Feb (5)	Mar (4)	Apr	May (10)	Jun (2)	Jul (9)	Aug (2)	Sep	Oct (4)	Nov (3)	Dec (2)
2015	Jan (4)	Feb (13)	Mar (6)	Apr (15)	May (8)	Jun (6)	Jul (3)	Aug	Sep (2)	Oct (3)	Nov (9)	Dec
2016	Jan	Feb (5)	Mar (7)	Apr (1)	May	Jun	Jul (2)	Aug (7)	Sep (7)	Oct (2)	Nov (8)	Dec (1)
2017	Jan (7)	Feb (5)	Mar (5)	Apr	May (1)	Jun (1)	Jul (5)	Aug (3)	Sep	Oct	Nov (5)	Dec (4)
2018	Jan (1)	Feb (8)	Mar (1)	Apr (2)	May	Jun (2)	Jul	Aug (1)	Sep (8)	Oct (4)	Nov (1)	Dec
2019	Jan	Feb (1)	Mar (1)	Apr (2)	May	Jun	Jul	Aug	Sep	Oct	Nov	Dec (2)
2020	Jan (1)	Feb	Mar (2)	Apr	May	Jun (2)	Jul (1)	Aug	Sep	Oct	Nov (1)	Dec (1)
2021	Jan	Feb	Mar	Apr (1)	May	Jun (1)	Jul	Aug	Sep	Oct	Nov	Dec
2022	Jan	Feb	Mar (2)	Apr	May	Jun	Jul	Aug	Sep (2)	Oct	Nov	Dec
2024	Jan (1)	Feb	Mar	Apr	May (1)	Jun	Jul	Aug	Sep	Oct	Nov	Dec
2025	Jan	Feb	Mar	Apr (1)	May	Jun	Jul	Aug	Sep	Oct	Nov	Dec

mummer-help Mailing List for MUMmer (Page 2)

mummer-help — For general MUMmer questions and help.