<div dir="ltr">Hi Devs,<br><div><br></div><div>When can I expect an update on these questions (Q7 and Q8)?</div><div><br></div><div>Thanks a lot!</div><div><br></div><div>Cheers, RM</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, 13 Sep 2019 at 17:53, Ramiro Magno <<a href="mailto:ramiro.magno@gmail.com">ramiro.magno@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Thank you Brandon for the information!<br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, 13 Sep 2019 at 17:38, Brandon Walts <<a href="mailto:bwalts@ebi.ac.uk" target="_blank">bwalts@ebi.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Hi Ramiro</p>
<p>Apologies for the delay. We have some answers for you now, and
more will be forthcoming:</p>
<p>Q1: This endpoint should work for most species. I have seen the
errors that sometimes arise, and we think suspect (but have not
confirmed) that there may be a bug in the TranscriptMapper that
supports this in the underlying Perl API. We will look into this
further.</p>
<p>Q2: No, but this is a good suggestion and we will look into
possibly implementing this.</p>
<p>Q3: Yes, only transcript IDs are valid for this endpoint.</p>
<p>Q4 and Q5: For the first part of your question, basically yes.
Gap represents a gap in the sequence. We will look into whether
setting the "overrun" to a gap is the desired behaviour, or
whether there may be a better way to return a result for a query
that goes beyond the end of a transcript.</p>
<p>Best<br>
-Brandon<br>
</p>
<div class="gmail-m_-6185895876161707102gmail-m_-4241928598382362686moz-cite-prefix">On 10/09/2019 14:21, Ramiro Magno
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Devs,<br>
<div><br>
</div>
<div>I have a few questions about the endpoint
"map/cdna/:id/:region".</div>
<div><br>
</div>
<div>Q1: How can I find what species work with this endpoint?</div>
<div><br>
</div>
</div>
</blockquote>
<blockquote type="cite">
<div dir="ltr">
<div>Q2: Is there a way of specifying the "range" parameter so
that it starts at 1 and goes till the end of the cDNA
sequence? E.g., 1..end?</div>
<div><br>
</div>
</div>
</blockquote>
<blockquote type="cite">
<div dir="ltr">
<div>Q3: In the doc, the description of the "id" parameter reads
"An Ensembl stable ID". But only transcript ids are valid
choices, correct? For example, making the nonsensical query
with a gene id gives back a not so tidy error: <a href="https://rest.ensembl.org/map/cdna/ENSG00000115263/1..1000?content-type=application/json;include_original_region=1" target="_blank">https://rest.ensembl.org/map/cdna/ENSG00000115263/1..1000?content-type=application/json;include_original_region=1</a>.</div>
</div>
</blockquote>
<blockquote type="cite">
<div dir="ltr">
<div><br>
</div>
<div>Q4: What is the meaning of the variable "gap" in the json
response? Is it gap=0 means exon, and gap=1 un-mappable
region? When I exceed the end position of the transcript in
the "range" parameter I always get the excess as a region
flagged as gap=1.</div>
</div>
</blockquote>
<blockquote type="cite">
<div dir="ltr">
<div><br>
</div>
<div>Q5: When I get an excess region as a result of asking a
cDNA sequence that goes beyond the length of transcript, why
are the genomic coordinates "start" and "end" reported as if
they were in cdna coordinate system? E.g., the request: <a href="https://rest.ensembl.org/map/cdna/ENST00000375497/1..1000?content-type=application/json;include_original_region=1" target="_blank">https://rest.ensembl.org/map/cdna/ENST00000375497/1..1000?content-type=application/json;include_original_region=1</a> yields
a last block whose coordinates are start=800, end=1000 for
both coordinate systems: "cdna" and "chromosome". Would it not
make more sense to just report NA or Null instead?</div>
</div>
</blockquote>
<blockquote type="cite">
<div dir="ltr">
<div><br>
</div>
<div>Q6: What is the meaning of the "rank" variable in the json
output?</div>
</div>
</blockquote>
<blockquote type="cite">
<div dir="ltr">
<div><br>
</div>
<div>Many thanks in advance!</div>
<div><br>
</div>
<div>Cheers, Ramiro</div>
</div>
<br>
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