<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi John,<br>
<br>
The zebrafish geneset contains 10 genes of biotype TEC (To be
Experimentally Confirmed)<br>
As such, they do not fit in any of the biotype categories we display
on the annotation page (they are not coding, not non coding, not
pseudogenes)<br>
<br>
The annotation page hence displays a count of 31,943 genes (25,642
coding, 6,008 non coding and 293 pseudogenes)<br>
The biomart page displays a count of 31,953 genes, which is the same
as the above + 10 TEC<br>
<br>
If you use the API with a fetch_all('toplevel'), this will retrieve
all chromosomes as well as all non assembled scaffolds.<br>
Using this with the same snippet of code that you include in your
email should return 31,953 genes, the same as biomart.<br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 07/12/2015 02:41, john samuel wrote:<br>
</div>
<blockquote cite="mid:5664F1C1.3030203@senecacollege.ca" type="cite">
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
Thanks Dan.<br>
I must admit I don't use biomart, so I don't know what it can do,
but now that you've shown me I see what you mean.<br>
That gives me a better idea about which total to use.<br>
Maybe someone else can shed some light on why the total on the
annotation page is different?<br>
John<br>
<br>
On 15-12-06 09:24 PM, Daniel Lawson wrote:
<blockquote
cite="mid:CAMwWv1wB_6ZwdkjSHo5cAAnmG51qapYUV2N9iehhwe2h1pnOqA@mail.gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<div dir="ltr">
<div class="gmail_default"
style="font-family:verdana,sans-serif">Hi John,</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif"><br>
</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif">You are missing 565
loci correct (31953 - 31388). </div>
<div class="gmail_default"
style="font-family:verdana,sans-serif"><br>
</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif">I open Mart and using
the Region filter select all non-chromosome scaffolds. The
'Gene' count for these is 565, see image if that works on
the email list, else I include a URL for the Mart query.</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif"><br>
</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif">
<pre style="color:rgb(0,0,0)"><a moz-do-not-send="true" href="http://www.ensembl.org/biomart/martview/68b3c7a216540966e2b2f569b596e7e6?VIRTUALSCHEMANAME=default&ATTRIBUTES=drerio_gene_ensembl.default.feature_page.ensembl_gene_id%7Cdrerio_gene_ensembl.default.feature_page.ensembl_transcript_id&FILTERS=drerio_gene_ensembl.default.filters.chromosome_name">http://www.ensembl.org/biomart/martview/68b3c7a216540966e2b2f569b596e7e6?VIRTUALSCHEMANAME=default&ATTRIBUTES=drerio_gene_ensembl.default.feature_page.ensembl_gene_id|drerio_gene_ensembl.default.feature_page.ensembl_transcript_id&FILTERS=drerio_gene_ensembl.default.filters.chromosome_name</a>."KN149679.1,KN149681.1,KN149682.1,KN149684.1,KN149686.1,KN149687.1,KN149688.1,KN149689.1,KN149690.1,KN149691.1,KN149694.1,KN149695.1,KN149696.1,KN149697.1,KN149698.1,KN149702.1,KN149704.1,KN149706.1,KN149707.1,KN149710.1,KN149711.1,KN149713.1,KN149715.1,KN149717.1,KN149719.1,KN149725.1,KN149727.1,KN149730.1,KN14
9731.1,KN
14
9732.1,KN149734.1,KN149735.1,KN149739.1,KN149753.1,KN149755.1,KN149764.1,KN149765.1,KN149776.1,KN149779.1,KN149781.1,KN149782.1,KN149784.1,KN149787.1,KN149790.1,KN149795.1,KN149797.1,KN149798.1,KN149799.1,KN149803.1,KN149813.1,KN149816.1,KN149818.1,KN149829.1,KN149830.1,KN149831.1,KN149842.1,KN149843.1,KN149846.1,KN149847.1,KN149850.1,KN149855.1,KN149857.1,KN149858.1,KN149859.1,KN149861.1,KN149868.1,KN149874.1,KN149878.1,KN149880.1,KN149883.1,KN149884.1,KN149886.1,KN149894.1,KN149895.1,KN149896.1,KN149897.1,KN149900.1,KN149904.1,KN149906.1,KN149909.1,KN149910.1,KN149912.1,KN149914.1,KN149916.1,KN149917.1,KN149921.1,KN149923.1,KN149929.1,KN149930.1,KN149933.1,KN149934.1,KN149936.1,KN149939.1,KN149943.1,KN149945.1,KN149946.1,KN149947.1,KN149948.1,KN149951.1,KN149955.1,KN149959.1,KN149962.1,KN149964.1,KN149966.1,KN149968.1,KN149978.1,KN149986.1,KN149987.1,KN149989.1,KN149992.1,KN149995.1,KN149997.1,KN149998.1,KN150000.1,KN150001.1,KN150002.1,KN150003.1,KN150008.1,KN150013.1,KN15
0015.1,KN
150027.1,KN150032.1,KN150038.1,KN150039.1,KN150040.1,KN150041.1,KN150042.1,KN150046.1,KN150051.1,KN150052.1,KN150056.1,KN150062.1,KN150064.1,KN150066.1,KN150067.1,KN150071.1,KN150072.1,KN150075.1,KN150079.1,KN150080.1,KN150084.1,KN150086.1,KN150088.1,KN150090.1,KN150096.1,KN150099.1,KN150102.1,KN150104.1,KN150108.1,KN150109.1,KN150112.1,KN150115.1,KN150120.1,KN150125.1,KN150127.1,KN150128.1,KN150131.1,KN150137.1,KN150141.1,KN150142.1,KN150148.1,KN150156.1,KN150158.1,KN150162.1,KN150164.1,KN150165.1,KN150168.1,KN150169.1,KN150170.1,KN150171.1,KN150172.1,KN150173.1,KN150176.1,KN150177.1,KN150178.1,KN150188.1,KN150189.1,KN150193.1,KN150196.1,KN150199.1,KN150205.1,KN150207.1,KN150208.1,KN150212.1,KN150213.1,KN150214.1,KN150216.1,KN150221.1,KN150229.1,KN150230.1,KN150232.1,KN150239.1,KN150240.1,KN150241.1,KN150251.1,KN150259.1,KN150262.1,KN150265.1,KN150267.1,KN150269.1,KN150272.1,KN150273.1,KN150277.1,KN150285.1,KN150305.1,KN150307.1,KN150311.1,KN150312.1,KN150314.1,KN150317.1,KN
150320.1,
KN150322.1,KN150324.1,KN150326.1,KN150328.1,KN150332.1,KN150334.1,KN150335.1,KN150336.1,KN150339.1,KN150342.1,KN150345.1,KN150346.1,KN150348.1,KN150350.1,KN150351.1,KN150353.1,KN150355.1,KN150359.1,KN150361.1,KN150362.1,KN150365.1,KN150366.1,KN150371.1,KN150372.1,KN150379.1,KN150380.1,KN150383.1,KN150387.1,KN150390.1,KN150399.1,KN150400.1,KN150401.1,KN150402.1,KN150403.1,KN150405.1,KN150407.1,KN150411.1,KN150412.1,KN150415.1,KN150416.1,KN150424.1,KN150425.1,KN150432.1,KN150433.1,KN150435.1,KN150442.1,KN150447.1,KN150449.1,KN150451.1,KN150456.1,KN150470.1,KN150474.1,KN150475.1,KN150482.1,KN150487.1,KN150490.1,KN150491.1,KN150492.1,KN150505.1,KN150506.1,KN150508.1,KN150516.1,KN150518.1,KN150521.1,KN150527.1,KN150530.1,KN150531.1,KN150532.1,KN150541.1,KN150543.1,KN150544.1,KN150545.1,KN150550.1,KN150552.1,KN150561.1,KN150562.1,KN150564.1,KN150566.1,KN150568.1,KN150570.1,KN150572.1,KN150574.1,KN150576.1,KN150578.1,KN150589.1,KN150590.1,KN150596.1,KN150597.1,KN150600.1,KN150603.1,
KN150605.
1,KN150608.1,KN150614.1,KN150616.1,KN150617.1,KN150620.1,KN150628.1,KN150630.1,KN150631.1,KN150635.1,KN150636.1,KN150637.1,KN150642.1,KN150647.1,KN150650.1,KN150653.1,KN150654.1,KN150663.1,KN150665.1,KN150666.1,KN150667.1,KN150670.1,KN150672.1,KN150674.1,KN150677.1,KN150680.1,KN150681.1,KN150683.1,KN150685.1,KN150691.1,KN150696.1,KN150698.1,KN150699.1,KN150700.1,KN150702.1,KN150703.1,KN150706.1,KN150708.1,KN150709.1"&VISIBLEPANEL=filterpanel</pre>
</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif"><br>
</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif">Hope that helps/goes
some way to explaining the difference between Mart and your
API script. I can't comment on whether or not either of
these are the definitive gene count for zebrafish.</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif"><br>
</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif">regards</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif">Dan</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif"><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 7 December 2015 at 02:17, john
samuel <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:john.samuel@senecacollege.ca"
target="_blank">john.samuel@senecacollege.ca</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> Thanks Dan.<br>
I thought of that, and I tried the same code but looking
for genes in all the scaffolds, thinking that there
might be some unplaced scaffolds, but the total for all
scaffolds adds up to 31,501. This could be, as you
said, all the genes mapped to chromosomes, plus some
unplaced scaffolds, but that doesn't match any of the
other totals, so I'm no closer to knowing which total is
correct.<br>
Any other thoughts?<span class="HOEnZb"><font
color="#888888"><br>
John</font></span>
<div>
<div class="h5"><br>
<br>
On 15-12-06 09:07 PM, Daniel Lawson wrote:
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_default"
style="font-family:verdana,sans-serif">Hi
John,</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif"><br>
</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif">There
may be other sequences in the assembly that
have not been assigned to a chromosome. You
can check this via the API or in Mart. I
expect you'll find a bunch of small sequences
that harbour some genes - maybe that will get
your totals to balance.</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif"><br>
</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif">cheers</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif">Dan</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif"><br>
</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif"><br>
</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif"><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 7 December 2015 at
01:59, john samuel <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:john.samuel@senecacollege.ca"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:john.samuel@senecacollege.ca">john.samuel@senecacollege.ca</a></a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> Hi,<br>
I am trying to get an accurate count of
all the ENSDARG genes from the latest
zebrafish data (<span>GRCz10) in ensembl.<br>
If I use the perl api to get all the
genes in all the chromosomes I get a
total of 31,388 i.e.<br>
<br>
my $slice_adaptor =
$registry->get_adaptor(
'danio_rerio', 'Core', 'Slice' );<br>
my @slices = @{
$slice_adaptor->fetch_all('chromosome')
};<br>
my $total = 0;<br>
my %all;<br>
foreach my $slice (@slices) {<br>
my @genes = @{
$slice->get_all_Genes() };<br>
my $count = scalar @genes;<br>
$all{$slice->seq_region_name()}=$count;<br>
$total += $count;<br>
}<br>
foreach my $sorted (sort {$a<=>$b}
keys %all) {<br>
print "chromosome:
$sorted\t$all{$sorted}\n";<br>
}<br>
print "gene total is\t$total\n";<br>
<br>
chromosome: MT 37<br>
chromosome: 1 1386<br>
chromosome: 2 1587<br>
chromosome: 3 1611<br>
chromosome: 4 3103<br>
chromosome: 5 1704<br>
chromosome: 6 1280<br>
chromosome: 7 1507<br>
chromosome: 8 1216<br>
chromosome: 9 1108<br>
chromosome: 10 1108<br>
chromosome: 11 1039<br>
chromosome: 12 952<br>
chromosome: 13 1013<br>
chromosome: 14 953<br>
chromosome: 15 1146<br>
chromosome: 16 1241<br>
chromosome: 17 1048<br>
chromosome: 18 942<br>
chromosome: 19 1123<br>
chromosome: 20 1253<br>
chromosome: 21 1092<br>
chromosome: 22 1174<br>
chromosome: 23 1031<br>
chromosome: 24 800<br>
chromosome: 25 934<br>
gene total is 31388<br>
<br>
Anyone see anything wrong with how I get
the total? I don't, but then when I go
to biomart (see below), I get a total of
31953<br>
<br>
</span><img
src="cid:part4.05020703.06090504@ebi.ac.uk"
alt=""><br>
<span><br>
and if I go to the info page for the
genome at <a moz-do-not-send="true"
href="http://useast.ensembl.org/Danio_rerio/Info/Annotation"
target="_blank">http://useast.ensembl.org/Danio_rerio/Info/Annotation</a>
I see a </span><span>different</span><span>
total there too (31,650 not counting
pseudogenes).<br>
<br>
</span><img
src="cid:part6.05090803.09080006@ebi.ac.uk"
alt=""><br>
<span><br>
Anyone have any idea why the different
totals and which one to believe and
whether there's anything wrong with
using the one that my code calculated as
the definitive one? I need to compare
the total number of genes vs. the number
that we are finding under certain
conditions, to do some stats.<span><font
color="#888888"><br>
John<br>
</font></span></span><br>
<br>
<br>
</div>
<br>
_______________________________________________<br>
Dev mailing list <a
moz-do-not-send="true"
href="mailto:Dev@ensembl.org"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a></a><br>
Posting guidelines and subscribe/unsubscribe
info: <a moz-do-not-send="true"
href="http://lists.ensembl.org/mailman/listinfo/dev"
rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a moz-do-not-send="true"
href="http://www.ensembl.info/"
rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div>
<div dir="ltr">
<div>VectorBase | i5K insect genome
initiative</div>
</div>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
<pre>_______________________________________________
Dev mailing list <a moz-do-not-send="true" href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a moz-do-not-send="true" href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a moz-do-not-send="true" href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
</div>
</div>
</div>
<br>
_______________________________________________<br>
Dev mailing list <a moz-do-not-send="true"
href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a
moz-do-not-send="true"
href="http://lists.ensembl.org/mailman/listinfo/dev"
rel="noreferrer" target="_blank"><a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a></a><br>
Ensembl Blog: <a moz-do-not-send="true"
href="http://www.ensembl.info/" rel="noreferrer"
target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div class="gmail_signature">
<div dir="ltr">
<div>VectorBase | i5K insect genome initiative</div>
</div>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</body>
</html>