How to download lincRNAs list (human) from RefSeq database ?

Question

[Ashley]

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

Answer 1

[EagleEye]

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/

[Ashley]

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!

[EagleEye]

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

[Ashley]

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！

[Ashley]

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

Answer 2

[Ashley]

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.