bedToBigBed with bed9 format
Fan, Yiping
Hello,
I converted bed 9 format file into bigBed using following command:
bedToBigBed -as=bedDes.as -type=bed9 chr22.bed hg19.chrom.sizes chr22.bb
I got the following error:
column #9 names do not match: Yours=[color] BED Standard=[reserved]
asObjects differ.
bedDes.as:
table hg19CG
"CG "
(
string chrom; "Reference sequence chromosome or scaffold"
uint chromStart; "CpG start position"
uint chromEnd; "CpG end position"
string name; "Name of CpG"
uint score; "Score"
char[1] strand; "+ or - for strand"
uint thickStart; "CpG start"
uint thickEnd; "CpG end"
string color; "color for methylation status"
)
Part of my bed file:
chr22 16050173 16050174 CpG 0 + 16050173 16050174 0,0,0
chr22 16050205 16050206 CpG 0 + 16050205 16050206 105,105,105
chr22 16050212 16050213 CpG 0 + 16050212 16050213 105,105,105
Please advise. Thanks!
Yiping Fan, Ph.D.
St. Jude Children's Research Hospital
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Mail Stop 1135
Memphis, TN 38105
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Fan, Yiping
Hi, Matthew,
Thanks! I tried your approach. I can’t see color in dense mode. but I can the color in other mode such as pack, squish.
track type="bigBed 9" itemRgb=on
I also tried:
track type="bigBed" itemRgb=on
It did not work either.
by the way, I can see color by using original bed file in all display modes including dense mode.
Yiping
From: Matthew Speir [mailto:msp...@soe.ucsc.edu]
Sent: Friday, August 02, 2013 3:31 PM
To: Fan, Yiping
Cc: gen...@soe.ucsc.edu
Subject: Re: [genome] bedToBigBed with bed9 format. .
--
Hello Yiping,
Thank you for your question about the bedToBigBed utility. If you look at our Data File Formats FAQ page under the bed section,http://genome.ucsc.edu/FAQ/FAQformat.html#format1, you will see that you are using the standard bed9 format as your input. Since your bed9 only contains standard bed fields, you do not need to use an AutoSQL (.as) file as part of your bedToBigBed input. You should get the output you are looking for if you run the following command:
bedToBigBed -type=bed9 chr22.bed hg19.chrom.sizes chr22.bb
For more information on creating bigBed files from bed files, refer to the bigBed format help page, http://genome.ucsc.edu/goldenPath/help/bigBed.html.
I hope this information is helpful. If you have further questions, please reply to gen...@soe.ucsc.edu.
Matt Speir
UCSC Genome Bioinformatics Group
Matthew Speir
--
Matthew Speir
Hello Yiping,
I'm glad that the previous solution worked! For bigBed files, there are a maximum number of items that can be in the current view before it will start using the summary data, which does not include coloring. This means that if you have zoomed out to view a large portion of a chromosome with a large number of items, you will not see any coloration. This parameter, maxItems, defaults to 250, but it can be set much higher in the track line when uploading the custom track. While this number can be set much higher than 250, it is not recommended to be set too high because of stability issues. You can refer to the Track Line section, http://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK, of the Custom Track help page for more information on setting different track parameters.
I hope this information is helpful. If you have further
questions, please reply to gen...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
Fan, Yiping
Hi, Matthew,
Thanks for your help! The problem is the dense mode won’t show color even at a single site. But I can see the color in other display mode such as pack mode. It seems this is not a window issue.
Matthew Speir
If you could us send your custom track plus any track lines, that would help us in assessing the problem. If you do not feel comfortable in sharing this information with the rest of the list, you may reply to me directly.
Thank you.
Matthew Speir
UCSC Genome Bioinformatics Group