Re: [MUMmer-help] help

[Adam P. <am...@um...>]

Hello Hui,
For mapping contigs to a chromosome, I typically suggest delta-filter -q.
That will filter based on an alignment score that is computed as (length *
identity) to identify the best alignments for each contig.

Have you overcome your problems running the delta-filter program?

Best,
-Adam


On Fri, Apr 3, 2015 at 3:18 AM, che...@ge... <
che...@ge...> wrote:

> Dear sir,
>
> Good days for you.
>
> Sorry to trouble you, however, we meet problem when we used nucmer.
>
> We want to link the contig into chromsome basing on finished genome. Then
> we run nucmer packages of mumer.
> After aligning,  It is so hard for us to choose a standard to filter the
> alignment (Coverage or aligning length ???)
>
> Would you like to give us some suggestions?
>
> many thanks for your help
> best regards
> yours sincerely, hui
>
>
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