[Genome] location of .tpa files

[Donna Karolchik]

hi Jonathan,

I suspect you are looking for TPF (i.e. tiling path format) files...we don't 
know of any TPA files. If so, you can most likely get those from the NCBI site. 
We do have some tables with clone IDs that might contain the info you're looking 
for, e.g. chr*_gold or ctgPos, depending on the type of accession/level of 
assembly structure you want. You can download these from our downloads server at 
http://hgdownload.cse.ucsc.edu/.

-Donna
-----------------------------------
Donna Karolchik
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

----- Original Message ----- 
From: "Jonathan Miller" <jnthnmllr at gmail.com>
To: <genome at soe.ucsc.edu>
Sent: Monday, November 06, 2006 8:44 AM
Subject: [Genome] location of .tpa files


> Re: location of .tpa files
>
> Hi,
>
> The Sanger Center referred me to files they say I should be able to find at
> UCSC ftp site; I can't find them - can you help?
> Here is the message from the Sanger Center; my orginal query to them is
> below that (see >); could you also take a quick look at my query and
> indicate whether you think there may be better alternatives...
>
> many thanks
>
> jm
> -----------------------------------------------------------------------------------------------------------------------
> Sorry for the delay in getting back to you - I needed to check this with
> one of our mouse experts.
>
> *Apparently you need to get the tiling path for your chromosome, with the
> ids of all the clones used in the assembly. You can get this from the
> UCSC ftp site (listed as TPA files).
>
> *For each one, you can then check its status. Finished and unfinished
> clones (with HTG phase statuses) should be in the EMBL database.
> Sections without an HTG status are whole genome shotgun contigs
> assembled directly from reads, rather than actual clones - they should
> also be available from EMBL, though we're guessing you're not so
> interested in those.
>
> I hope this is the information you need. If not, do get back to us and
> we'll try to help further.
>
> Regards
>
> Anne Parker
> Ensembl Web Team
> ------------------------------------------------------------------------------------------------------------------------
>>
>> Hi,
>>
>> I am trying to identify the set of "finished" sequence that was
>>    assembled into the mouse and human genomes.
>>
>> In particular, I'd like to find all sequence that, for example, was
>>    used to assemble the mouse X chromosome.
>>
>> So that for every location in the assembled mouse X chromosome, I can
>>    identify a "finished" contig(s) (or possibly a set of reads) that
>>    corresponds to this location.
>>
>> It appeared to me that the appropriate set of sequences should be at:
>>
>> (e.g. for human)
>>
>> ftp://ftp.sanger.ac.uk/pub/sequences/human/Chr_X/
>>
>> however, it appears that there are sequences in the assembled genome
>>    (any recent version) that are not represented in this directoy.
>>
> *> My goal is to investigate whether certain observations that I have
>>    made about the assembled genome sequences, could in fact be
>>    artifacts of the process of assembly.
>>
>> So I would like to look at sets of sequences that cover the full mouse
>>    genome at least once (in its current assembly), but are still at
>>    pre-assembly stages. The full set of traces is probably too crude
>>    for my purposes (I'd want at the very least only high quality
>>    reads).
> *>
> *> If you are unable to advise, I'd be grateful if you could direct me
>>    towards someone who could (preferably a name and email address).
>>
> *> many thanks and best wishes
>>
>> jm
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