Re: [MUMmer-help] Formatting for multiple queries

[Adam P. <aph...@gm...>]

Hi Martin,
When the manual states nucmer can process multiple references and queries,
it is referring to multi-fasta input format:

>sequence1
ACGT
>sequence2
ACGT
>sequence3
ACGT
...

Nucmer does not accept more than one file for the reference and one file for
the query. All sequences included in the reference file will be taken
together as the "references" and all sequences in the query file will be
taken together as the "queries". If you have multiple fasta files, you can
simply append them together using 'cat' to make a multi-fasta file. Just be
sure each sequence has a unique sequence identifier (the string after the
'>' and up to the first space).

Hope this clears things up,
-Adam


On Fri, Jul 30, 2010 at 9:59 AM, Dr. Martin Selke <m....@gm...> wrote:

> Hello,
>
> Most of the time I was using NUCMER with just one reference and query. Now,
> for the first time I would like to add some queries to my NUCMER run. Could
> someone please add an example as how to format such an analysis when using
> NUCMER? I tried different things, relying on my knowledge on how to separate
> multiple strings in PERL, but all I got was an error message
>
> "USAGE: nucmer  [options]  <Reference>  <Query>
>
> Try '/home/stylo/MUMmer3.22/nucmer -h' for more information."
>
> The tutorial states, that it is possible to do analyses of multiple
> references and queries but all the examples are for one reference and query.
> So, how do I add a second and a third (...) query to my NUCMER run? I tried
> brackets around my queries, [,] and [.] with or without whitespaces. What am
> I doing wrong?
>
> Sincerly,
> Martin
>
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> Dr. Martin Selke
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