Question: Where Can I Download A File That Has All Ensembl Gene Ids, Transcript Ids, And Most Importantly Gene Symbols
0
gravatar for hicsuntdrac0nis
5.2 years ago by
hicsuntdrac0nis220 wrote:

So I'm kind of tired of always using these online conversions that have a limit for how long the input list is . . . .

Is there anywhere where I can download a file (like through UCSC Table Browser or something) to get every single transcript, gene, and gene symbol in mm10

In this format:

ENSMUSTxxxxx    [tab]    ENSMUGxxxxx    [tab]    Upf1
ENSMUSTxxxxx    [tab]    ENSMUGxxxxx    [tab]    Upf2
ENSMUSTxxxxx    [tab]    ENSMUGxxxxx    [tab]    Upf3a
ENSMUSTxxxxx    [tab]    ENSMUGxxxxx    [tab]    Upf3b
ENSMUSTxxxxx    [tab]    ENSMUGxxxxx    [tab]    Smg1
ADD COMMENTlink modified 3.8 years ago by phil.chapman70 • written 5.2 years ago by hicsuntdrac0nis220
4
gravatar for Neilfws
5.2 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

Yes, this is quite easy using UCSC Table Browser or the UCSC public MySQL server.

Using Table Browser, fill in the fields so as they look like this (you may want to enter a file name):

enter image description here

Then, click "get output" and link to the ensemblToGeneName table, so as the fields look like this:

enter image description here

Click "get output" again; here are the first few lines of output:

#mm10.ensGene.name    mm10.ensGene.name2    mm10.ensemblToGeneName.value
ENSMUST00000086465    ENSMUSG00000042429    Adora1
ENSMUST00000038191    ENSMUSG00000042429    Adora1
ENSMUST00000169927    ENSMUSG00000042429    Adora1
ENSMUST00000132064    ENSMUSG00000025909    Sntg1
ENSMUST00000140295    ENSMUSG00000025909    Sntg1
ENSMUST00000140302    ENSMUSG00000025909    Sntg1
ENSMUST00000115484    ENSMUSG00000025909    Sntg1
ENSMUST00000135046    ENSMUSG00000025909    Sntg1
ENSMUST00000115488    ENSMUSG00000025909    Sntg1
ADD COMMENTlink written 5.2 years ago by Neilfws48k

you're a BOSS! thanks this is exactly what i was looking for

ADD REPLYlink written 5.2 years ago by hicsuntdrac0nis220
4
gravatar for Ashutosh Pandey
5.2 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

In case you are comfortable with command line then you can try Neilfws's solution on command line.

mysql --user=genome -N --host=genome-mysql.cse.ucsc.edu -A -D mm10  -e "select name,name2 from ensGene" > Gene1_table
mysql --user=genome -N --host=genome-mysql.cse.ucsc.edu -A -D mm10  -e "select name,value from mm10.ensemblToGeneName" > Gene2_table
paste Gene1_table Gene2_table > mm10_ensembl.txt
ADD COMMENTlink modified 5.2 years ago by Neilfws48k • written 5.2 years ago by Ashutosh Pandey11k
3

Can also do a single SQL query on the 2 tables, e.g.

select ensGene.name, name2, value from ensGene, ensemblToGeneName where ensGene.name = ensemblToGeneName.name
ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by Neilfws48k

I tried for that but couldn't somehow make it to work. Thanks a lot.

ADD REPLYlink written 5.2 years ago by Ashutosh Pandey11k
1
gravatar for Devon Ryan
5.2 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

It's probably easiest to just use biomart. I setup an example query here. Just click on "results" in the upper left for the first 10 (there's an option to export everything to a text file).

There's also an R interface to biomart, which can be handy.

ADD COMMENTlink written 5.2 years ago by Devon Ryan89k
1
gravatar for phil.chapman
3.8 years ago by
phil.chapman70
United Kingdom
phil.chapman70 wrote:

Check out the AnnotationHub package in R/Bioconductor.  This way you can easily download and access within R all sorts of annotation in just a few lines of code.  See the below presentation from the recent CSAMA 15 workshop for some more detail:

http://bioconductor.org/help/course-materials/2015/CSAMA2015/lect/L15-annotation-rsrcs-morgan-demo.html

These two short YouTube clips are also a good place to start:

Cheers,

Phil

ADD COMMENTlink written 3.8 years ago by phil.chapman70
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