long non coding RNAs annotation file

Question

[annaA]

Hello,

I am working with RNAseq data and currently I am using the wTO package in order to create expression networks. So I am interested on long non coding RNAs nad TFs . I already have a TFs annotation list and now I am searching for an updated lncRNAs list. does someone has to recommend something?

The format I need : Chromosome gene start gene end gene symbol UCSC ids +/or any other id is published

Thank you all, A

Answer 1

[GenoMax]

You can choose from GFF or BED format files from RNACentral for the genome you are interested in. You may need to extract lncRNA if that is all you are interested in.

[annaA]

Thank you I checked it already

Answer 2

[matt.a.bennett25890]

Think FANTOM CAT lncRNA database is most extensive, if you filter to those with stringently annotated start sites then it also has some nice experimental validation too

Otherwise think GENCODE references are seen as more conservative and curated than most whilst still being quite extensive and a good starting annotation set.

For converting to UCSC IDs would try this tool: https://biodbnet-abcc.ncifcrf.gov/db/db2db.php

[annaA]

Thanks a lot about the info

[annaA]

Hello,

just a small question about FANTOM so I filtered for lncRNA but is it possible to have the start and end site or its not provided ?

thank you in advance