Thanks for the update! I am not in a huge rush, but I was worried I
had not been describing the problem clearly, as it took quite a while
to explain to colleagues here :)
best

On Tue, Apr 24, 2012 at 3:24 PM, Jennifer Jackson <j...@bx.psu.edu> wrote:
> Hi Sarah,
>
> We appreciate all of the information you have provided and have been working
> here since yesterday to investigate the issue in more detail. This includes
> incorporating the additional data both you and Peter have been posting.
>
> We don't have anything conclusive to report yet, but it would have been
> considerate to send an update this morning to let you know what we were
> doing. Please accept my apologies for not doing so - we are in fact in
> complete agreement that as the data currently presents, something odd
> appears to be going on.  Genbank updates would be unrelated as gi numbers do
> not change through time (although they can be retired, but again, not
> related to this case). The question of the mismatch in the wrapped Megablast
> output between gi and reported length is the open issue to be addressed.
>
> A reply will be send as soon as the root cause is determined. If there is
> indeed a problem, this would of course be considered a priority to correct.
> Not that we are expecting delays, but if your analysis is very urgent, using
> the BLAST+ BLASTN megablast wrapper that Peter authored, in a local or cloud
> instance, would be the best immediate remedy (this version has the standard
> 12 column output). Sequence length data could always be obtained from
> Genbank and added into these results using other Galaxy tools (column join,
> etc.).
>
> Thank you and Peter both for the help and for your patience!
>
> Best,
>
> Jen
> Galaxy team
>
>
>
>
> On 4/24/12 1:50 PM, Sarah Hicks wrote:
>>
>> So, Jen, I'm not sure if we're talking about the same ID change... I
>> am under the impression that GenBank does not change it's GI numbers
>> for it's entries. Plus, it's now looking like all sequence length
>> output info for each hit through Galaxy's megablast does not match to
>> the GI number output given by Galaxy megablast, but to the GI number
>> before it. Because the "-1" rule is so consistent, it makes this seem
>> less and less like it has to do with NCBI changing it's GI numbers to
>> make room for new entries or something. In other words, there is a
>> shift, as if a 1 was added to each NCBI GI number in galaxy before
>> galaxy produces the output file.
>>
>> I need someone to tell me if I can trust the output. Basically I see
>> it this way. Every hit row from Galaxy megablast actually has
>> information for two NCBI entries: the one that shares the GI output
>> and the one before it that shares the sequence length output. Which
>> one is the hit I should be using?
>> Because on some occations, the NCBI entry that shares the GI output
>> from galaxy is VERY distantly related to the NCBI entry that shares
>> the subject sequence length output from galaxy, and I don't know which
>> to pick. Is this problem well understood, yet?
>>
>>
>> On Tue, Apr 24, 2012 at 10:52 AM, Peter Cock<p.j.a.c...@googlemail.com>
>>  wrote:
>>>
>>> On Mon, Apr 23, 2012 at 11:41 PM, Sarah Hicks<garlicsc...@gmail.com>
>>>  wrote:
>>>>
>>>> Peter, you requested an example, here are the first five hits for my
>>>> first query sequence (OTU#0)
>>>>
>>>> 0       324034994       527     93.23   266     13      5       1
>>>> 265     22      283     7e-102  379.0
>>>> 0       56181650        513     93.26   267     10      8       1
>>>> 265     25      285     7e-102  379.0
>>>> 0       314913953       582     91.79   268     13      9       1
>>>> 265     24      285     2e-92   347.0
>>>> 0       305670062       281     92.52   254     14      5       4
>>>> 256     32      281     2e-92   347.0
>>>> 0       310814066       1180    91.73   266     14      7       1
>>>> 265     24      282     9e-92   345.0
>>>>
>>>> You will notice there are 13 columns, one in addition to the 12 column
>>>> titles you explained. This is because there is a column between sseqID
>>>> and pident.
>>>
>>>
>>> I see now - the megablast_wrapper.py calls megablast (from the old legacy
>>> NCBI blast suite) which does indeed produce 12 column tabular output. But
>>> the wrapper script then edits the output:
>>>
>>> It appears to be splitting column 2 in two at the underscore intended to
>>> give the match ID and the length. This puzzles me but I haven't used
>>> the legacy BLAST tabular output for a while. On BLAST+ you can ask
>>> for the query or subject length explicitly as their own columns so we
>>> don't have this problem.
>>>
>>> The megablast_wrapper.py also re-formats the floating point score in the
>>> last column, apparently the NCBI style could cause problems with the
>>> Galaxy filter tool.
>>>
>>>> In the metagenomic tutorial the first 4 columns are
>>>> explained, and column 3 is described as length of sequence in database
>>>> (or length of the subject sequence).
>>>>
>>>> This is the problem column. The length of only one of the subject GI
>>>> numbers above match the subject length in NCBI. This has caused me to
>>>> wonder if I can trust the hit info. In all cases that I've checked,
>>>> when this happens the correct match is the listed GI value minus 1
>>>> (ie, in NCBI, gi|324034994 is not 527nt long, but 324034993 IS 527nt
>>>> long).
>>>
>>>
>>> That is strange.
>>>
>>> Peter
>>
>>
>
> --
> Jennifer Jackson
> http://galaxyproject.org

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