<div dir="ltr">Thanks Keiron<div><br></div><div>But this still leaves me with a question.</div><div><br></div><div>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?</div><div><br></div><div>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?</div><div><br></div><div>Thanks</div><div><br></div><div>Duarte</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><font style="background-color:rgb(255,255,255)" color="#999999">=========================<br> Duarte Miguel Paulo Molha <br></font><div><font style="background-color:rgb(255,255,255)" color="#999999"> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a> <br>=========================</font></div></div></div>
<br><div class="gmail_quote">On 10 March 2015 at 15:22, Kieron Taylor <span dir="ltr"><<a href="mailto:ktaylor@ebi.ac.uk" target="_blank">ktaylor@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Duarte,<br>
<br>
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.<br>
<br>
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.<br>
<br>
<br>
Regards,<br>
<br>
Kieron<br>
<br>
<br>
Kieron Taylor PhD.<br>
Ensembl Core senior software developer<br>
<br>
EMBL, European Bioinformatics Institute<br>
<div><div class="h5"><br>
<br>
<br>
<br>
<br>
> On 10 Mar 2015, at 11:57, Duarte Molha <<a href="mailto:duartemolha@gmail.com">duartemolha@gmail.com</a>> wrote:<br>
><br>
> Dear developers<br>
><br>
> I have a script that I wrote (in attachment) that gets me the refseq exons for give input gene<br>
><br>
> However when I use this code using the gene ASXL1 as an example is:<br>
><br>
> <a href="http://test_query.pl" target="_blank">test_query.pl</a> ASXL1<br>
><br>
> QueryName feature_type common_name Biotype id chr start end strand<br>
> ASXL1 Exon ASXL1 protein_coding NM_001164603.1.1 chr20 30946147 30946635 +<br>
> ASXL1 Exon ASXL1 protein_coding NM_001164603.1.2 chr20 30954187 30954269 +<br>
> ASXL1 Exon ASXL1 protein_coding NM_001164603.1.3 chr20 30955530 30955532 +<br>
> ASXL1 Exon ASXL1 protein_coding NM_001164603.1.4 chr20 30956818 30956926 +<br>
> ASXL1 Exon ASXL1 protein_coding NM_015338.5.5 chr20 31015931 31016051 +<br>
> ASXL1 Exon ASXL1 protein_coding NM_015338.5.6 chr20 31016128 31016225 +<br>
> ASXL1 Exon ASXL1 protein_coding NM_015338.5.7 chr20 31017141 31017234 +<br>
> ASXL1 Exon ASXL1 protein_coding NM_015338.5.8 chr20 31017704 31017856 +<br>
> ASXL1 Exon ASXL1 protein_coding NM_015338.5.9 chr20 31019124 31019287 +<br>
> ASXL1 Exon ASXL1 protein_coding NM_015338.5.10 chr20 31019386 31019482 +<br>
> ASXL1 Exon ASXL1 protein_coding NM_015338.5.11 chr20 31020683 31020788 +<br>
> ASXL1 Exon ASXL1 protein_coding NM_015338.5.12 chr20 31021087 31021720 +<br>
> ASXL1 Exon ASXL1 protein_coding NM_015338.5.13 chr20 31022235 31027122 +<br>
><br>
><br>
> As you can see, I am missing some of the exons for transcript NM_015338.5<br>
> 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 :<br>
><br>
> ASXL1 Exon ASXL1 protein_coding NM_015338.5.1 chr20 30946147 30946635 +<br>
> ASXL1 Exon ASXL1 protein_coding NM_015338.5.2 chr20 30954187 30954269 +<br>
> ASXL1 Exon ASXL1 protein_coding NM_015338.5.3 chr20 30955530 30955532 +<br>
><br>
> Can you tell me what is wrong with my approach and how I can retrieve the missing data?<br>
><br>
> Best regards<br>
><br>
> Duarte<br>
</div></div>> <<a href="http://test_query.pl" target="_blank">test_query.pl</a>>_______________________________________________<br>
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</blockquote></div><br></div>