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Old 07-15-2010, 09:32 AM   #1
jjw14
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Default UCSC Table Browser: Please tell me there is an easier way...

With the advice of several members of the SEQanswers forum and a lot of reading, I was able to go from Illumina ChIP-seq reads to viewing alignments in the UCSC Genome Browser - Thanks! Also, a huge thanks to the UCSC team for a great resource.

I thought the next step would be easy (I can hear the chuckling now): I want to analyze these data with the UCSC Table Browser to determine the number of reads that align to different features (e.g. CpG islands). My custom tracks are in BAM format and I keep getting errors when I try to add them to the Table Browser (e.g. # No results returned from query).

Then I converted my BAM files to BED files, but the upload to UCSC times out when I use the following URL format (without the "-" at the beginning):

-http://genome.ucsc.edu/cgi-bin/hgTracks?db=susScr2&position=chr7&hgt.customText=http://mysite.edu/MyReads.bed

Now I am about to try to convert my BED files to BigBED format. Before I do this, is there an easier way to just view my BAM files in the Table Browser that I am just not seeing (or more likely, a mistake I am making)?

Many thanks in advance,
jjw
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Old 07-15-2010, 09:44 AM   #2
epigen
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If you just want to "determine the number of reads that align to different features" and produce a output BED or BAM file that is not that big, you could do that locally with BEDTools (code.google.com/p/bedtools/).
There are entries about the tools on the forum and the developer is also active here (quinlana).

Last edited by epigen; 07-15-2010 at 09:47 AM. Reason: should mention the support here
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Old 07-15-2010, 10:45 AM   #3
jjw14
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That does sound more direct than the Rube Goldberg method I was attempting.

Just so I am clear, would something like this be correct:

$ intersectBed -a MyReads.bed -b CpGIslands.bed

where the CpGIslands.bed file contains the output from the CpG Island data downloaded from the UCSC Table Browser?

If that's true, you've saved me a lot of time However, I still like all of the options the Table Browser provides.

Thank you for the prompt reply,
jjw
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Old 07-16-2010, 01:05 AM   #4
epigen
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I'm not sure if the CpG Island data downloaded from the UCSC Table Browser are in BED format, but if they are, your command should work.
I agree that the Table Browser is nice to use, especially because you don't have to download all the files. But when I needed a real intersection, i.e. all info of both tables combined, I was not so happy with it. BEDTools has much more options for this.
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Old 07-16-2010, 05:54 AM   #5
jjw14
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Yes, UCSC's Table Browser does have BED format as a file output option. I've been reading the excellent BEDTools documentation by the developer, Aaron Quinlan, that you mentioned. I have to agree with you that BEDTools is very flexible and powerful. Thanks so much again for the information.

jjw
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Old 07-19-2010, 07:39 AM   #6
bioinfosm
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I would vouch for bedTools too. And the downloaded .bed files, like exons, or CpG in your case, are not that huge after all!
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