[Genome] (no subject)

[Kayla Smith]

Shop,


Here's our FAQ on liftOver:
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Convert

I couldn't say why the particular regions you're trying to lift are 
failing, but there are a few failure messages you might see along with 
their explanations, on the web interface:

http://genome.ucsc.edu/cgi-bin/hgLiftOver?hglft_errorHelp=1

Deleted in new:
     None of sequence intersects with any alignment chain for the region
Partially deleted in new:
     Sequence intersects with part of a single alignment chain in the region
Split in new:
     Sequence partially intersects multiple chains in the region
Duplicated in new:
     Sequence completely intersects multiple chains in the region
Boundary problem:
     Missing start or end base in an exon

I hope this helps to explain the error message you're seeing.   Please 
don't hestitate to contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group


Swapan Mallick wrote:
> Hello,
> 
> Liftover works like a charm and is amazingly quick.
> But occasionally it fails, generating entries for unmapped.txt.
> 
> I'd like to know why it fails - could you please tell me / point me to
> some documentation?
> 
> Shop
> 
> 
>> You can use a pipe and then use stdin as the input e.g.
>>
>> cat test.bed | liftOver stdin hg16ToHg18.over.chain lifted.bed
>> unmapped.txt
>>
>> Rachel
>>
>> Rachel Harte
>> UCSC Genome Bioinformatics Group
>> http://genome.ucsc.edu
>>
>>
>> On Thu, 19 Apr 2007, Swapan Mallick wrote:
>>
>>>
>>> Oh! it takes a file as an input -
>>> are there any versions available which take a pipe? (my sequences are
>>> not
>>> in bed format, so I have to convert them - passing through a pipe would
>>> be
>>> much more efficient that building temporary files)
>>>
>>>
>>> Shop
>>>
>>>
>>>> Hello,
>>>>
>>>> Here is a link to where you can download the precompiled executables
>>> for
>>>> liftOver:
>>>>
>>>> http://hgdownload.cse.ucsc.edu/admin/exe/
>>>>
>>>> Rachel
>>>>
>>>> Rachel Harte
>>>> UCSC Genome Bioinformatics Group
>>>> http://genome.ucsc.edu
>>>>
>>>>
>>>> On Thu, 19 Apr 2007, Swapan Mallick wrote:
>>>>
>>>>> Hello again,
>>>>>
>>>>> I have two questions:
>>>>>
>>>>> 1)
>>>>> By any chance do you have precompiled executables for: ia64 linux?
>>>>>
>>>>> Amazingly, we don't have mysql installed so compiling from source
>>> fails
>>>>> (
>>>>> at the point when jkhgap.a is being made ).
>>>>>
>>>>> Alternatively, is there a way of building liftOver without mysql. In
>>> the
>>>>> meantime I'm trying to get mysql installed but it may not be a quick
>>>>> process here.
>>>>>
>>>>> 2)
>>>>> Is there any detailed documentation on how liftOver works?
>>> Conceptually
>>>>> it
>>>>> sounds like it should be a trivial problem, but I'm sure there are
>>> many
>>>>> details I'm not aware of.
>>>>>
>>>>> We plan to process many billions of sequences which makes error
>>> checking
>>>>> non-trivial, and I'd like to know more about what any pitfalls might
>>> be.
>>>>>
>>>>> Shop
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> Hello Shop Mallick,
>>>>>>
>>>>>> To convert from hg16 to hg18 coordinates, you will only need to use
>>>>> one
>>>>>> liftOver chain file and that is hg16ToHg18.over.chain. You can
>>>>> download
>>>>>> this file from the downloads server by clicking on the link to
>>>>> LiftOver
>>>>>> files in the human hg16 section or go directly to:
>>>>>>
>>>>>> http://hgdownload.cse.ucsc.edu/goldenPath/hg16/liftOver/
>>>>>>
>>>>>> I hope that this helps you. Please let us know if you have further
>>>>>> questions.
>>>>>>
>>>>>> Rachel
>>>>>>
>>>>>> Rachel Harte
>>>>>> UCSC Genome Bioinformatics Group
>>>>>> http://genome.ucsc.edu
>>>>>>
>>>>>>
>>>>>> On Wed, 18 Apr 2007, Swapan Mallick wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> I'm working at the genetics department in the Harvard Medical
>>> School.
>>>>>>> We have a set of alignments which were created for version 16 of
>>> the
>>>>>>> human
>>>>>>> genome. We wish to map these to version 18, and I would like to
>>> build
>>>>>>> wrappers around the liftover tool to do this.
>>>>>>>
>>>>>>> I have already downloaded the chain file:
>>>>>>> hg18ToHg17.over.chain
>>>>>>>
>>>>>>> But I think I need the corresponding files: hg16ToHg18.over.chain
>>> .
>>>>> Is
>>>>>>> this available?
>>>>>>>
>>>>>>> Best regards,
>>>>>>> Shop Mallick
>>>>>>>
>>>>>>>
>>>>>>> ---------------------------------------------------------
>>>>>>> Dr Swapan 'Shop' Mallick
>>>>>>> Dept. of Genetics
>>>>>>> Harvard Medical School, NRB
>>>>>>> 77 Avenue Louis Pasteur
>>>>>>> Boston, MA 02115
>>>>>>> Tel: +1-617-432-5993
>>>>>>> Email: shop at genetics.med.harvard.edu
>>>>>>> ---------------------------------------------------------
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Genome maillist  -  Genome at soe.ucsc.edu
>>>>>>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>>>>>>>
>>>>>>
>>>>>
>>>>> ---------------------------------------------------------
>>>>> Dr Swapan 'Shop' Mallick
>>>>> Dept. of Genetics
>>>>> Harvard Medical School, NRB
>>>>> 77 Avenue Louis Pasteur
>>>>> Boston, MA 02115
>>>>> Tel: +1-617-432-5993
>>>>> Email: shop at genetics.med.harvard.edu
>>>>> ---------------------------------------------------------
>>>>>
>>>>
>>>
>>> ---------------------------------------------------------
>>> Dr Swapan 'Shop' Mallick
>>> Dept. of Genetics
>>> Harvard Medical School, NRB
>>> 77 Avenue Louis Pasteur
>>> Boston, MA 02115
>>> Tel: +1-617-432-5993
>>> Email: shop at genetics.med.harvard.edu
>>> ---------------------------------------------------------
>>>
>>
> 
> 
> ---------------------------------------------------------
> Dr Swapan 'Shop' Mallick
> Dept. of Genetics
> Harvard Medical School, NRB
> 77 Avenue Louis Pasteur
> Boston, MA 02115
> Tel: +1-617-432-5993
> Email: shop at genetics.med.harvard.edu
> ---------------------------------------------------------
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome