[ensembl-dev] question regarding refseq exons retreival
Duarte Molha
duartemolha at gmail.com
Wed Mar 11 16:32:38 GMT 2015
Thanks Magali
Are there any plans to correct the naming structure of your refseq imports?
Take as an example the transcript NM_001164603 associated with gene ASXL1
On your main database you have associated it with transcript ID ENST00000497249
that has a transcript length of 296 bp and 5 exon
ENST00000497249
<http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000171456;r=20:32358811-32372242;t=ENST00000497249>
However, the true refseq transcript is stored in your other features as a
novel transcript with the correct identifier
NM_001164603.1
<http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=otherfeatures;g=171023;r=20:32358344-32372549;t=NM_001164603.1>
It contains 5 exons but a transcript length of 1070bp
however,
In that table you call the transcript with the correct REFSEQ_ID, but then
on the exon layer, you pick different identifiers for exons 2,3 and 4 of
this transcript!
NM_001164603.1.1
<http://www.ensembl.org/Homo_sapiens/Location/View?db=otherfeatures;g=171023;r=20:32358294-32358882;t=NM_001164603.1>
XM_006723729.1.2
<http://www.ensembl.org/Homo_sapiens/Location/View?db=otherfeatures;g=171023;r=20:32366334-32366516;t=NM_001164603.1>
XM_006723729.1.3
<http://www.ensembl.org/Homo_sapiens/Location/View?db=otherfeatures;g=171023;r=20:32367677-32367779;t=NM_001164603.1>
XM_006723729.1.4
<http://www.ensembl.org/Homo_sapiens/Location/View?db=otherfeatures;g=171023;r=20:32368965-32369173;t=NM_001164603.1>
NM_001164603.1.5
<http://www.ensembl.org/Homo_sapiens/Location/View?db=otherfeatures;g=171023;r=20:32372114-32372599;t=NM_001164603.1>
Many thanks
Duarte
=========================
Duarte Miguel Paulo Molha
http://about.me/duarte
=========================
On 11 March 2015 at 09:35, mag <mr6 at ebi.ac.uk> wrote:
> Hi Duarte,
>
> I am not convinced all genes in Ensembl will have at least one mapping to
> RefSeq, but your snippet of code should work regardless.
>
>
> Regards,
> Magali
>
> On 10/03/2015 17:05, Duarte Molha wrote:
>
> Thanks ... I think I have understood
>
> Just confirm one thing to me ...
>
> if I get all ensembl transcripts of any given gene at least one of those
> transcripts will have a database mapping to refseq correct?
>
> for example ... consider the code:
>
> $transcripts = $gene->get_all_Transcripts(); while ( my $transcript =
> shift @{$transcripts} ) { my %transcripts_refseq_ids = (); foreach my $dbe
> (@{ $transcript->get_all_DBEntries() }) { if($dbe->dbname() eq
> "RefSeq_mRNA") { $transcripts_refseq_ids{ $dbe->display_id() } = 1; } } }
>
> I should be confident that by cycling through all ensembl transcripts of
> a gene and checking for a mRNA refseq entry I should be able to pull out
> all transcripts that map . Correct?
>
> Thanks
>
> Duarte
>
>
> =========================
> Duarte Miguel Paulo Molha
> http://about.me/duarte
> =========================
>
> On 10 March 2015 at 16:20, mag <mr6 at ebi.ac.uk> wrote:
>
>> Hi Duarte,
>>
>> It is important to bear in mind that Ensembl and RefSeq transcripts are
>> different objects.
>>
>> There is a large overlap between the two resources, but small differences
>> in coding sequence and UTRs mean that there is not always a one-to-one
>> mapping between an Ensembl transcript and a RefSeq transcript.
>> This also means that an Ensembl transcript might overlap some RefSeq
>> exons, but not all.
>>
>> In your use-case however, you should be able to get the information you
>> want by replacing the following call:
>> $gene->get_all_DBLinks( 'RefSeq_mRNA')
>> with $transcript->get_all_DBEntries('RefSeq_mRNA')
>>
>> RefSeq_mRNA corresponds to RefSeq transcripts, which we consequently map
>> to Ensembl transcripts.
>> With your current script, you are fetching all genes where at least one
>> transcript is mapped to a RefSeq transcript.
>> Instead, you can directly fetch only the transcripts which have a mapping
>> to RefSeq.
>>
>>
>> Hope that helps,
>> Magali
>>
>> On 10/03/2015 15:30, Duarte Molha wrote:
>>
>> Thanks Keiron
>>
>> But this still leaves me with a question.
>>
>> Say that I have a gene, and I retreive the correct gene object from the
>> ensembl database. How can I output only the transcripts that are referenced
>> in Refseq is not my the way I have done it?
>>
>> If I go the normal way, the $gene->get_all_Transcripts(); method will
>> retrieve all ensembl transcripts. How can I limit it to only get
>> transcripts that are refseq?
>>
>> Thanks
>>
>> Duarte
>>
>> =========================
>> Duarte Miguel Paulo Molha
>> http://about.me/duarte
>> =========================
>>
>> On 10 March 2015 at 15:22, Kieron Taylor <ktaylor at ebi.ac.uk> wrote:
>>
>>> Dear Duarte,
>>>
>>> The issue you have exposed is subtle. You seem to be printing “exon
>>> stable IDs” but expecting them to be RefSeq accessions. Our mistake was to
>>> use the RefSeq IDs as arbitrary identifiers for internal use, but I must
>>> stress the what Ensembl calls a Stable ID must never be assumed to have any
>>> meaning outside of an Ensembl database. What you want are display labels.
>>> The exon labels were generated by picking only the first of any possible
>>> RefSeq IDs, hence you cannot get everything you want in this way.
>>>
>>> The correct way to handle this in your code is to fetch the transcript
>>> name and print that in each exon, as RefSeq IDs refer to transcripts and
>>> not exons.
>>>
>>>
>>> Regards,
>>>
>>> Kieron
>>>
>>>
>>> Kieron Taylor PhD.
>>> Ensembl Core senior software developer
>>>
>>> EMBL, European Bioinformatics Institute
>>>
>>>
>>>
>>>
>>>
>>> > On 10 Mar 2015, at 11:57, Duarte Molha <duartemolha at gmail.com> wrote:
>>> >
>>> > Dear developers
>>> >
>>> > I have a script that I wrote (in attachment) that gets me the refseq
>>> exons for give input gene
>>> >
>>> > However when I use this code using the gene ASXL1 as an example is:
>>> >
>>> > test_query.pl ASXL1
>>> >
>>> > QueryName feature_type common_name Biotype id chr
>>> start end strand
>>> > ASXL1 Exon ASXL1 protein_coding NM_001164603.1.1 chr20
>>> 30946147 30946635 +
>>> > ASXL1 Exon ASXL1 protein_coding NM_001164603.1.2 chr20
>>> 30954187 30954269 +
>>> > ASXL1 Exon ASXL1 protein_coding NM_001164603.1.3 chr20
>>> 30955530 30955532 +
>>> > ASXL1 Exon ASXL1 protein_coding NM_001164603.1.4 chr20
>>> 30956818 30956926 +
>>> > ASXL1 Exon ASXL1 protein_coding NM_015338.5.5 chr20
>>> 31015931 31016051 +
>>> > ASXL1 Exon ASXL1 protein_coding NM_015338.5.6 chr20
>>> 31016128 31016225 +
>>> > ASXL1 Exon ASXL1 protein_coding NM_015338.5.7 chr20
>>> 31017141 31017234 +
>>> > ASXL1 Exon ASXL1 protein_coding NM_015338.5.8 chr20
>>> 31017704 31017856 +
>>> > ASXL1 Exon ASXL1 protein_coding NM_015338.5.9 chr20
>>> 31019124 31019287 +
>>> > ASXL1 Exon ASXL1 protein_coding NM_015338.5.10 chr20
>>> 31019386 31019482 +
>>> > ASXL1 Exon ASXL1 protein_coding NM_015338.5.11 chr20
>>> 31020683 31020788 +
>>> > ASXL1 Exon ASXL1 protein_coding NM_015338.5.12 chr20
>>> 31021087 31021720 +
>>> > ASXL1 Exon ASXL1 protein_coding NM_015338.5.13 chr20
>>> 31022235 31027122 +
>>> >
>>> >
>>> > As you can see, I am missing some of the exons for transcript
>>> NM_015338.5
>>> > In this case, the 1st 3 exons of transcript NM_015338.5 are identical
>>> to NM_001164603.1, but I would expect to have them listed as :
>>> >
>>> > ASXL1 Exon ASXL1 protein_coding NM_015338.5.1 chr20
>>> 30946147 30946635 +
>>> > ASXL1 Exon ASXL1 protein_coding NM_015338.5.2 chr20
>>> 30954187 30954269 +
>>> > ASXL1 Exon ASXL1 protein_coding NM_015338.5.3 chr20
>>> 30955530 30955532 +
>>> >
>>> > Can you tell me what is wrong with my approach and how I can retrieve
>>> the missing data?
>>> >
>>> > Best regards
>>> >
>>> > Duarte
>>> > <test_query.pl>_______________________________________________
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>>
>>
>>
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