Question: How to download lincRNAs list (human) from RefSeq database ?
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gravatar for Ashley
18 months ago by
Ashley40
China
Ashley40 wrote:

Dear all, In my project, I want to obtain the annotated long intergenic non-coding RNAs (lincRNAs) set. Among all kinds of representative annotation databases, I need a high quality set, RefSeq. However, I don't know how to download all lincRNAs from RefSeq in batch. Can you help me step by step? Thank you very much! It's very helpful for my research. sincerely, liuzhe

rna-seq next-gen gene genome • 662 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by Ashley40
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gravatar for EagleEye
18 months ago by
EagleEye6.1k
Sweden
EagleEye6.1k wrote:

I can suggest you to use,

1) Gencode 'Long non-coding RNA gene annotation'

http://www.gencodegenes.org/releases/current.html

2) Ensembl (Extract only lincRNA)

ftp://ftp.ensembl.org/pub/release-89/gtf/homo_sapiens/

3) noncode

http://www.noncode.org/download.php

4) FANTOM CAT

http://fantom.gsc.riken.jp/cat/

ADD COMMENTlink modified 18 months ago • written 18 months ago by EagleEye6.1k

I'm so sorry. I need a high quality set, RefSeq. Thanks a lot. But I really need a lincRNAs list from RefSeq. And good luck!

ADD REPLYlink written 18 months ago by Ashley40

May I know how you say Refseq as 'high quality set' (in which context) ??

Did you first of all check the links I provided ? All those repositories are standard repositories used for lncRNA analysis.

If you want information on refseq genes check Refseq FTP

ADD REPLYlink modified 18 months ago • written 18 months ago by EagleEye6.1k

All lncRNAs list I obtained from these four database and more (UCSC Genome Browser). But I really want to obtain other lncRNA set from other database, such as RefSeq. Because the number of all lncRNAs is lesser than others and it has more information than other, such as, linear or circular and so on. Thank you, but I really want to RefSeq lincRNA. And good luck!

ADD REPLYlink written 18 months ago by Ashley40

And I'm more interested in lincRNA as a part of lncRNAs.

ADD REPLYlink written 18 months ago by Ashley40
0
gravatar for Ashley
18 months ago by
Ashley40
China
Ashley40 wrote:

However, I don't know how to download all lincRNAs from RefSeq in batch. I can only search each lncRNA one by one via NCBI RefSeq database.

ADD COMMENTlink written 18 months ago by Ashley40
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