Question: How can I get .bed file that have unique Entrez gene id (or symbol) for deeptools?
0
gravatar for swordbreadjj
5.1 years ago by
Korea, Republic Of
swordbreadjj0 wrote:

Hi all, 

I want to get .bed file that contains unique gene id (Entrez id or gene symbol) for function of "computeMatrix reference-point" in deeptools.

 

like this

chr1    3204562 3661579 NM_001011874    Xkr4    -   
chr1    4481008 4486494 NM_011441   Sox17   -   
chr1    4763278 4775807 NM_001177658    Mrpl15  -   
chr1    4797973 4836816 NM_008866   Lypla1  + 

 

How or where can i get this file??

 

 

 

chip-seq • 2.9k views
ADD COMMENTlink modified 5.1 years ago by Jorge Amigo12k • written 5.1 years ago by swordbreadjj0
0
gravatar for Devon Ryan
5.1 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

If you happened to align against a reference genome from UCSC, then you can just download the refseq file from the table browser. This is the simplest method to get a BED12 file for computeMatrix.

If you aren't using a UCSC reference genome (we don't), you can construct the BED12 files as such (this is actually part of my reference genome Makefile):

  1. Download a GTF file from Ensembl/Gencode/UCSC/etc.
  2. I then use the the following, assuming the GTF file is called "annotation.gtf" and the BED file should be called "annotation.bed":
awk '{if ($$3 != "gene") print $$0;}' annotation.gtf | grep -v "^#" | /package/UCSCtools/gtfToGenePred /dev/stdin /dev/stdout | /package/UCSCtools/genePredToBed stdin annotation.bed

Practically speaking, I can also provide appropriate files for most common genomes (mouse, human, fly and worm). Since we developed deepTools, we have a lot of these and I probably just post whatever you need if you can't directly get it from UCSC.

ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by Devon Ryan97k

is it possible to use gtfToGenePred on gencode version?

ADD REPLYlink written 12 months ago by krushnach80850
0
gravatar for Jorge Amigo
5.1 years ago by
Jorge Amigo12k
Santiago de Compostela, Spain
Jorge Amigo12k wrote:

you can get that particular output directly from Ensembl at http://www.ensembl.org/biomart/martview/

> select Ensembl genes, homo sapiens (reference dependent)
> go to the attributes section
> unselect ensembl gene id, transcript id
> select chromosome, gene start, gene end, associated transcript name, associated gene name, strand
> export results

note that chromosome names won't have the "chr" suffix. add it if needed.

ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by Jorge Amigo12k
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