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

[Surya S. <ss...@co...>]

Hi Adam,

I discovered something interesting doing this round of tests. Consider this
excerpt from the .delta file produced by nucmer where BAC2:501-1001 is
aligned out of order on CHR01.
>CHR01 BAC2 20000 1500
183 683 501 1001 0 0 0
0
3001 3500 1 500 0 0 0
0
4001 4500 1001 1500 0 0 0
0
>CHR01 BAC5 20000 5050
683 3500 51 2868 0 0 0
0
4001 5000 2869 3868 0 0 0
0

Using delta-filter -g removes the out of order alignment so thats good.
>CHR01 BAC2 20000 1500
3001 3500 1 500 0 0 0
0
4001 4500 1001 1500 0 0 0
0
>CHR01 BAC5 20000 5050
683 3500 51 2868 0 0 0
0
4001 5000 2869 3868 0 0 0
0

Now if I add the -u flag to remove the non-unique alignments (delta-filter
-g -u 99), I expect none of the alignments to show up but the offending
alignment reappears
>CHR01 BAC2 20000 1500
183 683 501 1001 0 0 0
0

The order of precedence is "-i -l -u -q -r -g -m -1" so -g should chuck
this alignment out even if -u allows it. Am I missing something? Thanks
much.

-Surya




On Thu, Feb 12, 2015 at 3:06 PM, Adam Phillippy <aph...@gm...>
wrote:

> 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
>>
>
>


-- 

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