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

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

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