Hello, Danny,
You can do this using the Table Browser. Follow the
Tables link from the top bluebar and set the following
(these are the defaults if you have not been to the TB
before):
assembly: hg19
group: Genes and Gene Prediction Tracks
track: UCSC Genes
table: knownGene
Then, where it says, "identifiers", click the button
[paste list] and paste in
BACH1
BACH1
ZNRF1
...
[submit]
set output format: sequence [get output]
then select mRNA as sequence type.
You asked for the gene names associated with the transcripts
(which come out with our internal ucID when you ask for
sequence), so a second step is required:
With your list still loaded in the identifiers, go back
to the TB and switch to:
output format: selected fields from primary and related
tables
Then on the next page, check the boxes for the
table.field as follows:
knownGene.name
kgXref.geneSymbol
[get output]
You will have to do the substitution of the transcript
ucIDs to geneSymbol manually, or via a script.
best regards,
--b0b kuhn
ucsc genome bioinformatics group
On 3/22/2012 4:39 AM, Danny wrote:
> Hello all. I'd like to get the fasta sequences of all the human
> transcripts of some genes, with the official symbol provided by HGNC after
> the greater than symbol, e.g.:
>
>> BACH1 transcript 1
> (sequence)
>
>> BACH1 transcript 2
> (sequence)
>
>> ZNRF1 transcript 1
> (sequence)
>
> .....
>
> Can anyone give me a hint? I don't see a track of HGNC. Thanks.
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
