Combine all your individual chromosome .bed files into one single sorted .bed
file:
sort -k1,1 -k2,2n chr1.bed chr2.bed chr3.bed ... > hg19.sorted.bed
Now convert that file to a bigBed file:
bedToBigBed hg19.sorted.bed hg19.chrom.sizes hg19.yourData.bb
Place the resulting file hg19.yourData.bb on a WEB server so it can
be referenced via a URL. Use that URL in the 'bigDataUrl' specification
on your custom track line. There is only a single track line to submit
for this data. The bigDataUrl is used by the UCSC genome browser to
fetch data out of your bigBed file as needed. Note the usage message
from the bedToBigBed command:
$ bedToBigBed
bedToBigBed v. 4 - Convert bed file to bigBed.
usage:
bedToBigBed in.bed chrom.sizes out.bb
Where in.bed is in one of the ascii bed formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bb is the output indexed big bed file.
The in.bed file must be sorted by chromosome,start,
to sort a bed file, use the unix sort command:
sort -k1,1 -k2,2n unsorted.bed > sorted.bed
options:
-blockSize=N - Number of items to bundle in r-tree. Default 256
-itemsPerSlot=N - Number of data points bundled at lowest level. Default 512
-bedFields=N - Number of fields that fit standard bed definition. If
undefined
assumes all fields in bed are defined.
-as=fields.as - If have non-standard fields, it's great to put a definition
of each field in a row in AutoSql format here.
-rgbField=N - the Nth field is a comma separated R,G,B triple.
For the usual itemRgb/reserved bed field this is 9.
-unc - If set, do not use compression.
-tabs - If set, expect fields to be tab separated, normally
expects white space separator.
--Hiram
----- Original Message -----
From: "Minou Bina" <[email protected]>
To: "Luvina Guruvadoo" <[email protected]>
Cc: [email protected]
Sent: Monday, November 7, 2011 3:24:41 PM
Subject: [Genome] bed and bigbed files
It is not clear at all how one would create bigbed for all human chromosomes.
For a given track, do we put the results of all chromosomes in one bigbed or do
we make a bigbed for each chromosomes?
Minou Bina
Purdue University
----- Original Message -----
From: "Luvina Guruvadoo" <[email protected]>
To: "Minou Bina" <[email protected]>
Cc: [email protected]
Sent: Monday, November 7, 2011 4:45:09 PM
Subject: Re: [Genome] bed and bigbed files
Hi Minou,
If you have a large file, you may want to consider using the bigBed data
format. Please see the following page for more information on bigBed:
http://genome.ucsc.edu/goldenPath/help/bigBed.html
If you would like to share your bigBed data track with others, see this
page for details on how to create a URL:
http://genome.ucsc.edu/goldenPath/help/customTrack.html#SHARE
Please contact us again at [email protected] if you have any further
questions.
---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
On 11/1/2011 1:04 PM, Minou Bina wrote:
> Hi
>
> To create a custom track for the entire human genome
>
> It is not clear whether or not results for all chromosomes should be in a
> single .bed file
>
> If the track for all chromosomes is put in a single .bed file, could this
> .bed file be converted to bigbed so that the track could be accessed by
> other labs?
>
> Minou Bina
> Purdue University
> _______________________________________________
> 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
