Hi Hani,
You can further filter the list you retrieved via the table browser by
adding another parameter to your filter:
filter: click 'create' then in the 'name DOES match' field type: NR_*
and then scroll down to the 'AND Free-form query:' and
type: txEnd - txStart >=200
This will provide you with data for all non-coding RNAs that are greater
than or equal to 200 bp. You can change the "200" to whatever base-pair
number you consider to be the minimum base-pair length of long
non-coding RNAs.
To obtain the sequence for each long non-coding RNA, do the same query
(including the updated filter information I've provided above) but for
output select 'sequence.' After clicking 'get output' select 'mRNA' and
click submit.
I hope this information is helpful! Please don't hesitate to contact the
mail list again if you have any further questions.
Katrina Learned
UCSC Genome Bioinformatics Group
Hani Choudhry wrote, On 03/25/11 05:49:
> Dear UCSC,
> Thanks for your reply. The instructions were very helpful to download all non
> coding RNAs.
>
> However, I only want list of long non coding RNAs (name, Chromosomal
> location, strand and sequences) based on “NCBI 37/ Hg19”
>
> Or how can I isolate long non coding RNAs from all non coding RNA list?!
>
> This information will be very useful and I will be greatly appreciated your
> help.
>
> Thanks for your attention and look forward to your reply soon.
>
> Sincerely,
> Hani Choudhry
> ________________________________________
> From: Luvina Guruvadoo [[email protected]]
> Sent: 17 March 2011 19:52
> To: Hani Choudhry
> Cc: [email protected]
> Subject: Re: [Genome-mirror] Human lncRNA list
>
> Hi Hani,
>
> The information you are requesting can be retrieved using the Table
> Browser. Click on "Tables" on the blue bar on the top of the main page
> and make the following selections:
>
> clade: Mammal
> genome: Human
> assembly: hg19
> group: Genes and Gene Prediction Tracks
> track: RefSeqGenes
> table: refGene
> region: genome
> filter: click 'create' then in the 'name DOES match' field type: NR_*
> output format: select fields from primary and related tables
> output file: if you would rather have the results saved to a file
> instead of displaying in the browser window, enter the name you would
> like the output file to have, otherwise, leave blank
> file type returned: plain text
>
> Click "get output". From here, select the following: name, chrom,
> strand. Click "get output". This will provide a list of non-coding RNA
> names, positions, and strands. To retrieve sequences, go back to the
> table browser and set the same settings, except set 'output format' to
> 'sequence'.
>
> I hope this helps. Feel free to contact us again at [email protected]
> if you have further questions.
>
> ---
> Luvina Guruvadoo
> UCSC Genome Bioinformatics Group
>
>
> Hani Choudhry wrote:
>
>> Dear UCSC,
>> It is my pleasure to contact you. I am a PhD student, working on non-coding
>> RNA regulation in cancer, in particular long non-coding RNA.
>> I am wondering if you can help in downloading all Human long non-coding RNA
>> list (name, Chromosomal location, strand and sequences) based on “NCBI 37/
>> Hg19” from your website?!
>> This information will be very useful for my PhD project and I will be
>> greatly appreciated your help.
>> Thanks for your attention and look forward to your reply soon.
>> Sincerely,
>> Hani
>>
>> ..........................................................................
>>
>> Hani Choudhry,
>>
>> Genomic Research Lab
>>
>> Wellcome Trust Centre of Human Genetics
>>
>> Nuffield Dept of Clinical Medicine
>>
>> University of Oxford
>>
>> Oxford- UK
>>
>> Lab tel: +44-1865287519
>>
>> Mobile: +44-7771219664
>>
>> Email: [email protected]<mailto:[email protected]>
>> _______________________________________________
>> Genome-mirror mailing list
>> [email protected]
>> https://lists.soe.ucsc.edu/mailman/listinfo/genome-mirror
>>
>>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
