Re: [MUMmer-help] delta-filter parameters for out of order matches

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

Hi Surya,
Can you give me an example of an alignment (just the coords) that you want
to be filtered, but is left by delta-filter -g?

-Adam


On Thu, Feb 12, 2015 at 12:24 AM, Surya Saha <ss...@co...> wrote:

> Hi Adam,
>
> The delta-filter -g option with -u does not filter out the offending
> alignments in all cases. I think I will parse the delta file from nucmer to
> identify these out of order alignments unless there is a better option.
> Thank you for the prompt response!
>
> Best,
> Surya
> .
>
> On Wed, Feb 11, 2015 at 4:42 PM, Adam Phillippy <aph...@gm...>
> wrote:
>
>> Hi Surya,
>> See if the delta-filter -g option does what you want. That option will
>> enforce that the relative ordering of alignments on both the reference and
>> query is consistent.
>>
>> Best,
>> -Adam
>>
>>
>> On Wed, Feb 11, 2015 at 1:24 PM, Surya Saha <ss...@co...> wrote:
>>
>>> Hi Adam et al.,
>>>
>>> I am trying to use nucmer/delta-filter (v3.23) to align BACs to a
>>> chromosome with gaps (Ns) with a goal to find BACs that span gaps. I want
>>> to filter out any imperfect alignments. This also means any BAC that aligns
>>> out of order on the chromosome.
>>> Here is an example with out of order alignments (100% identity)
>>> BAC:100-200 aligns to CHR:500-600
>>> BAC:201-300 aligns to CHR:1001-1100
>>> BAC:301-400 aligns to 701-800
>>>
>>> I am trying to optimize delta-filter parameters for screening these out.
>>> I can screen out all alignments where a region of the chromosome is covered
>>> by multiple BACs with -u (99-100). Any ideas how to screen out the out of
>>> order alignments with delta-filter? Thanks!
>>>
>>>
>>> -Surya
>>>
>>>
>>> --
>>>
>>> Surya Saha
>>> Sol Genomics Network,
>>> Boyce Thompson Institute, Ithaca, NY, USA.
>>> Plant Pathology and Plant-Microbe Biology Section,
>>> Cornell University, NY, USA.
>>> http://www.linkedin.com/in/suryasaha
>>> https://twitter.com/SahaSurya
>>>
>>>
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>>
>
>
> --
>
> Surya Saha
> Sol Genomics Network,
> Boyce Thompson Institute, Ithaca, NY, USA.
> Plant Pathology and Plant-Microbe Biology Section,
> Cornell University, NY, USA.
> http://www.linkedin.com/in/suryasaha
> https://twitter.com/SahaSurya
>