Hi Jeremy
I have taken a look at a random few transcripts from your list and the
reason these are duplicated is because they lie in the pseudoautosomal
(PAR) regions. For release 64 we ran a post build script to add this
information to the mart database, however this has caused quite a bit
of confusion so we have decided to remove this information for release
65 due out in a few weeks. For more information about PAR regions you
might find this paper informative: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2435358/
. You can also take a look at these PAR regions in ensembl here:
http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000124334;r=X:155227246-155251689
I hope that helps but please don't hesitate to get back to me if you
require further information,
Regards
Rhoda
On 2 Nov 2011, at 18:06, Arek Kasprzyk wrote:
Hi Jeremy,
i am forwarding your email to the users mailing list. Rhoda and/or
Steffen may want to comment on those
a
On Wed, Nov 2, 2011 at 1:30 PM, Jeremy Leipzig <[email protected]>
wrote:
Hi Arek,
Can you look into if these Ensembl transcript names are somehow
duplicated in Biomart?
This is related to this Bioconductor question:
http://biostar.stackexchange.com/questions/13819/bioconductor-problem-with-maketranscriptdbfrombiomart-genomicfeatures-package
[1] "ENST00000244174" "ENST00000262640" "ENST00000285718"
"ENST00000286448" "ENST00000302805" "ENST00000313871"
[7] "ENST00000326153" "ENST00000331035" "ENST00000334060"
"ENST00000334651" "ENST00000340131" "ENST00000355432"
[13] "ENST00000355805" "ENST00000359512" "ENST00000361536"
"ENST00000369423" "ENST00000369437" "ENST00000381177"
[19] "ENST00000381180" "ENST00000381184" "ENST00000381187"
"ENST00000381192" "ENST00000381218" "ENST00000381222"
[25] "ENST00000381223" "ENST00000381229" "ENST00000381233"
"ENST00000381241" "ENST00000381261" "ENST00000381297"
[31] "ENST00000381317" "ENST00000381333" "ENST00000381401"
"ENST00000381469" "ENST00000381500" "ENST00000381507"
[37] "ENST00000381509" "ENST00000381524" "ENST00000381529"
"ENST00000381566" "ENST00000381567" "ENST00000381575"
[43] "ENST00000381578" "ENST00000381625" "ENST00000381657"
"ENST00000381663" "ENST00000390665" "ENST00000391707"
[49] "ENST00000399012" "ENST00000399966" "ENST00000400701"
"ENST00000400841" "ENST00000411342" "ENST00000412290"
[55] "ENST00000412516" "ENST00000412936" "ENST00000414513"
"ENST00000415337" "ENST00000416733" "ENST00000417535"
[61] "ENST00000419094" "ENST00000419737" "ENST00000420411"
"ENST00000420865" "ENST00000421233" "ENST00000422618"
[67] "ENST00000424344" "ENST00000425740" "ENST00000427886"
"ENST00000429181" "ENST00000430235" "ENST00000430536"
[73] "ENST00000430562" "ENST00000430923" "ENST00000431238"
"ENST00000431582" "ENST00000431919" "ENST00000432272"
[79] "ENST00000432318" "ENST00000432523" "ENST00000432757"
"ENST00000434938" "ENST00000435581" "ENST00000436474"
[85] "ENST00000437244" "ENST00000441131" "ENST00000443019"
"ENST00000443929" "ENST00000444280" "ENST00000445062"
[91] "ENST00000445777" "ENST00000445785" "ENST00000445792"
"ENST00000447472" "ENST00000447786" "ENST00000448477"
[97] "ENST00000449611" "ENST00000452144" "ENST00000453953"
"ENST00000455739" "ENST00000456370" "ENST00000460206"
[103] "ENST00000460621" "ENST00000460672" "ENST00000461007"
"ENST00000461691" "ENST00000462195" "ENST00000463317"
[109] "ENST00000463763" "ENST00000464205" "ENST00000464935"
"ENST00000467626" "ENST00000468169" "ENST00000469624"
[115] "ENST00000474361" "ENST00000474865" "ENST00000475167"
"ENST00000475259" "ENST00000475594" "ENST00000475859"
[121] "ENST00000476066" "ENST00000477110" "ENST00000477636"
"ENST00000477940" "ENST00000478256" "ENST00000478825"
[127] "ENST00000479401" "ENST00000479438" "ENST00000479687"
"ENST00000481245" "ENST00000482170" "ENST00000482293"
[133] "ENST00000482405" "ENST00000483079" "ENST00000483286"
"ENST00000483543" "ENST00000484026" "ENST00000484364"
[139] "ENST00000484415" "ENST00000484611" "ENST00000485332"
"ENST00000486791" "ENST00000488344" "ENST00000489233"
[145] "ENST00000491683" "ENST00000492963" "ENST00000493312"
"ENST00000494962" "ENST00000494969" "ENST00000496011"
[151] "ENST00000496301" "ENST00000496630" "ENST00000497752"
"ENST00000498153" "ENST00000501036" "ENST00000503018"
[157] "ENST00000507418" "ENST00000509780" "ENST00000515319"
"ENST00000527459" "ENST00000534940" "ENST00000540897"
[163] "ENST00000554971"
Thanks,
Jeremy
Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.
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